Diff of the two buildlogs: -- --- b1/build.log 2021-07-03 13:23:02.690583882 +0000 +++ b2/build.log 2021-07-03 13:47:03.299604831 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Aug 5 07:36:00 -12 2022 -I: pbuilder-time-stamp: 1659728160 +I: Current time: Sun Jul 4 03:23:07 +14 2021 +I: pbuilder-time-stamp: 1625318587 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 Wed Jan 2 01:51:35 2019 -12 +gpgv: Signature made Thu Jan 3 03:51:35 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking iqtree_1.6.9+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/39253/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/42517/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-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/42517/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/42517/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=16' - 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=15' + 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='6534fbfd2ca94614bace22c8e1a0af23' - 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='39253' - PS1='# ' - PS2='> ' + INVOCATION_ID=0f4cf3b358324b1399f4568b922e5e04 + 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=42517 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.tWVBNBrTnZ/pbuilderrc_udrE --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/b1 --logfile b1/build.log iqtree_1.6.9+dfsg-1.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + 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.tWVBNBrTnZ/pbuilderrc_wFQ8 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/b2 --logfile b2/build.log iqtree_1.6.9+dfsg-1.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://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) 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 Jul 24 02:46 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/39253/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 Jul 4 03:23 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 21 22:26 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/42517/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -309,7 +343,7 @@ Get: 99 http://deb.debian.org/debian buster/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get: 100 http://deb.debian.org/debian buster/main amd64 time amd64 1.7-25.1+b1 [31.6 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] -Fetched 39.4 MB in 1s (70.1 MB/s) +Fetched 39.4 MB in 1s (27.2 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.) @@ -741,7 +775,7 @@ 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/iqtree-1.6.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/iqtree-1.6.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 1.6.9+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -934,176 +968,149 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_build -Bbuild.omp - cd build.omp && make -j16 "INSTALL=install --strip-program=true" + cd build.omp && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/nclextra /build/iqtree-1.6.9+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/whtest /build/iqtree-1.6.9+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/sprng /build/iqtree-1.6.9+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/vectorclass /build/iqtree-1.6.9+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -Scanning dependencies of target lbfgsb -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -Scanning dependencies of target sprng Scanning dependencies of target gsl -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target kernelavx +Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -Scanning dependencies of target pllavx +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -Scanning dependencies of target ncl -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -Scanning dependencies of target vectorclass -Scanning dependencies of target whtest -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +Scanning dependencies of target pll make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -Scanning dependencies of target kernelfma -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target sprng +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -Scanning dependencies of target kernelsse -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -Scanning dependencies of target kernelavx -Scanning dependencies of target nclextra -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +Scanning dependencies of target ncl +Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -Scanning dependencies of target pll -[ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +Scanning dependencies of target kernelsse +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -[ 2%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp -[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c -[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp -[ 4%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -[ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c -[ 6%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -[ 7%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -[ 8%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 2%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +[ 3%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp +[ 4%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp +[ 5%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +[ 6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp +[ 7%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +[ 8%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c +[ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp +[ 9%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 10%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp -[ 11%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c -[ 12%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c -[ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c +[ 11%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp -[ 15%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c -[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -[ 15%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c -cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp -[ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c -[ 15%] Linking CXX static library libvectorclass.a +[ 11%] Linking CXX static library libvectorclass.a +[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - extern __inline unsigned int bitcount_64_bit(uint64_t i); - ^~~~~~~~~~~~~~~ +[ 12%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 17%] Linking C static library libsprng.a -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +[ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o -/usr/bin/ranlib libsprng.a -[ 17%] Built target vectorclass -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 18%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp -[ 19%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c -[ 19%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c -[ 19%] Built target sprng -[ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c -[ 21%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c +[ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c +[ 14%] Built target vectorclass +[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1115,27 +1122,33 @@ /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX static library libgsl.a +[ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c +[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp +[ 17%] Linking CXX static library libgsl.a cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c +[ 18%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a +In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: +/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + extern __inline unsigned int bitcount_64_bit(uint64_t i); + ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 22%] Built target gsl -[ 22%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c -[ 23%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp +[ 18%] Built target gsl +[ 19%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1153,7 +1166,6 @@ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ -[ 24%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign @@ -1166,16 +1178,27 @@ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ +[ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp +[ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp +[ 20%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c +[ 21%] Linking C static library libsprng.a +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c +cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o +/usr/bin/ranlib libsprng.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 21%] Built target sprng +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp +[ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c -[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1192,25 +1215,33 @@ /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp -[ 27%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +[ 24%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c +[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c +[ 26%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c -[ 27%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ -[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp -[ 28%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp +[ 28%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c +[ 28%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c +[ 29%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c -[ 28%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp +[ 30%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c -[ 29%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 31%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined @@ -1229,46 +1260,64 @@ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ -[ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c -In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -[ 31%] Linking C static library libpllavx.a +[ 33%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: -/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - extern __inline unsigned int bitcount_64_bit(uint64_t i); - ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp -[ 32%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 33%] Built target pllavx +[ 33%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp +[ 34%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -[ 32%] Built target pllavx /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp -[ 33%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o /usr/bin/ranlib liblbfgsb.a -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c [ 34%] Built target lbfgsb -[ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp -In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: +[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp +Scanning dependencies of target utils +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 36%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp +[ 36%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp +[ 36%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c +In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp +[ 38%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1285,8 +1334,6 @@ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign @@ -1299,111 +1346,107 @@ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp -[ 37%] Linking CXX static library libwhtest.a +[ 39%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp +[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp +[ 39%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp +[ 40%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 37%] Built target whtest -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -Scanning dependencies of target utils -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 38%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp -[ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c -In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp +[ 41%] Built target whtest +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp +[ 42%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c +In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 43%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp +[ 44%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp +[ 44%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c +[ 45%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp -[ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: +/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + extern __inline unsigned int bitcount_64_bit(uint64_t i); + ^~~~~~~~~~~~~~~ +[ 45%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c -[ 41%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c -[ 42%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp -[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp -[ 43%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c -[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 44%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +[ 47%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp +[ 47%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +[ 48%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c -[ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c +cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 45%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +[ 49%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c +[ 49%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c +[ 50%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 45%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp -[ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp -[ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 50%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c -In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: +[ 51%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c +In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp -[ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp -[ 49%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c -[ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp -[ 49%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c -In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: +In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +[ 51%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 50%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +[ 52%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c +[ 53%] Linking CXX static library libncl.a +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': @@ -1462,46 +1505,40 @@ /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp -[ 51%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp -[ 53%] Linking CXX static library libncl.a -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -[ 54%] Linking C static library libpll.a -cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libncl.a -/usr/bin/ranlib libpll.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 54%] Built target ncl +[ 53%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= -[ 54%] Built target pll Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +[ 53%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp -[ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o +[ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp +[ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -[ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp -[ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -[ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp -[ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +[ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp +[ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp +[ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp +[ 58%] Linking C static library libpll.a +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + ^~~~~ +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 58%] Built target pll [ 59%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 @@ -1520,15 +1557,12 @@ cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp -/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - ^~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o @@ -1538,8 +1572,8 @@ [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp @@ -1547,14 +1581,14 @@ cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp -[ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp -[ 68%] Linking CXX static library libutils.a +[ 67%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' @@ -1565,17 +1599,14 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp -[ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp +[ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1588,22 +1619,9 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1616,14 +1634,10 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelProtein::readRates(istream &in) throw(const char*, string) { - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1636,8 +1650,14 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelDNA::readRates(string str) throw(const char*) { + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1650,6 +1670,32 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelMarkov::readRates(istream &in) throw(const char*, string) { + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelMarkov::readRates(string str) throw(const char*) { + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelMarkov::readStateFreq(string str) throw(const char*) { + ^~~~~ +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1664,12 +1710,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1682,25 +1724,17 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelDNA::readRates(string str) throw(const char*) { +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelMarkov::readRates(istream &in) throw(const char*, string) { - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelMarkov::readRates(string str) throw(const char*) { - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelMarkov::readStateFreq(string str) throw(const char*) { - ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelProtein::readRates(istream &in) throw(const char*, string) { + ^~~~~ +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o @@ -1713,19 +1747,19 @@ cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp +[ 76%] Linking CXX static library libpda.a +cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +/usr/bin/ranlib libpda.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 76%] Built target pda [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp -[ 77%] Linking CXX static library libpda.a -cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 78%] Built target pda [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o @@ -1734,8 +1768,6 @@ cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1750,12 +1782,16 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1770,8 +1806,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -1797,8 +1831,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ -[ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1834,8 +1866,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, - from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: +[ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1848,6 +1884,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: @@ -1868,10 +1910,8 @@ /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: +In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, + from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1884,12 +1924,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -1946,40 +1980,37 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -[ 84%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp -[ 84%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 84%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp +[ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp -In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: +In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, + from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -1992,9 +2023,9 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp +In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2007,9 +2038,24 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp +/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: + from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2022,16 +2068,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp -/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -2045,8 +2081,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -2061,20 +2095,20 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 97%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp -[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp -/build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - ^~~~~~~~ +[ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ +/build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -2136,128 +2170,126 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.serial - cd build.serial && make -j16 "INSTALL=install --strip-program=true" + cd build.serial && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend +Scanning dependencies of target kernelavx +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target gsl +Scanning dependencies of target ncl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +Scanning dependencies of target kernelfma +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +Scanning dependencies of target pllavx +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build +[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -Scanning dependencies of target pllavx Scanning dependencies of target nclextra +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +Scanning dependencies of target vectorclass +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build Scanning dependencies of target sprng +Scanning dependencies of target pll +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -Scanning dependencies of target vectorclass -Scanning dependencies of target ncl +cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp +Scanning dependencies of target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +Scanning dependencies of target kernelsse make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp -Scanning dependencies of target kernelavx -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp -Scanning dependencies of target kernelsse -[ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c -[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp -[ 3%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 3%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp -[ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c +[ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -[ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp -Scanning dependencies of target pll cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp -[ 6%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -[ 7%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp +[ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp -[ 8%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -Scanning dependencies of target kernelfma -cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c +cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp +[ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +[ 7%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -[ 9%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp -[ 10%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +[ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c -[ 11%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp +[ 9%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c +[ 10%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp +[ 11%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp +[ 11%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: @@ -2270,12 +2302,47 @@ cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c -[ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 15%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c +[ 16%] Linking CXX static library libgsl.a +cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c +cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp +[ 16%] Built target vectorclass +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp +[ 17%] Built target gsl +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +[ 18%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c +[ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp +In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: +/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + extern __inline unsigned int bitcount_64_bit(uint64_t i); + ^~~~~~~~~~~~~~~ +[ 19%] Linking C static library libsprng.a +cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o +/usr/bin/ranlib libsprng.a In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2287,42 +2354,49 @@ /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - extern __inline unsigned int bitcount_64_bit(uint64_t i); - ^~~~~~~~~~~~~~~ -[ 15%] Linking CXX static library libgsl.a -[ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c -cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c -cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -/usr/bin/ranlib libgsl.a -[ 17%] Built target vectorclass -[ 17%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c +[ 19%] Built target sprng +[ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp +[ 21%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 18%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c -[ 18%] Built target gsl -[ 18%] Building C object pll/CMakeFiles/pll.dir/hash.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c -[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -[ 19%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp +[ 23%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c +[ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp +[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp +[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c +[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c +[ 27%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2352,6 +2426,37 @@ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ +[ 28%] Linking C static library libpllavx.a +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp +[ 29%] Built target pllavx +[ 30%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp +[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp +[ 31%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 31%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 32%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c +Scanning dependencies of target utils +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 33%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2368,25 +2473,26 @@ /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ +[ 34%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Linking C static library libsprng.a -cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -[ 21%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +[ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp +[ 35%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c +[ 36%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp +[ 37%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c -cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o -/usr/bin/ranlib libsprng.a -[ 21%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp +[ 37%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 21%] Built target sprng -[ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o -[ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2404,22 +2510,35 @@ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ -[ 23%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c +[ 38%] Building C object pll/CMakeFiles/pll.dir/models.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 23%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +[ 38%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp +[ 39%] Linking CXX static library libwhtest.a +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +/usr/bin/ranlib libwhtest.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 39%] Built target whtest +[ 39%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c -[ 24%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +[ 40%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp +[ 41%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c -[ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp +[ 42%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2448,126 +2567,109 @@ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp -[ 27%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +[ 43%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c -[ 28%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +[ 43%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c -[ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 29%] Linking C static library libpllavx.a -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 29%] Built target pllavx -[ 30%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c -[ 31%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 43%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp +[ 44%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp +[ 45%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c -[ 31%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c -[ 32%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 32%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c -In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: +[ 46%] Linking CXX static library libnclextra.a +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 +/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +/usr/bin/ranlib libnclextra.a +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 46%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +Scanning dependencies of target pda +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 47%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c +[ 47%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp +In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: +[ 48%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp +[ 48%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c +In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 33%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -[ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp +[ 50%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 35%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 35%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c -Scanning dependencies of target utils -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -[ 36%] Building C object pll/CMakeFiles/pll.dir/stack.c.o -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c -[ 37%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp +[ 51%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 37%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 51%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c +[ 52%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c +[ 52%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c -[ 38%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c -[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp -[ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +[ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp +[ 54%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c +[ 54%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c +[ 55%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c +[ 56%] Linking CXX static library libncl.a +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 40%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c -[ 41%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp -[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp +cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +/usr/bin/ranlib libncl.a In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': @@ -2626,131 +2728,63 @@ /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp -[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp -[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp -[ 44%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp -[ 44%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp -[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp -[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp -[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp -[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp -[ 48%] Linking CXX static library libwhtest.a -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -[ 49%] Linking C static library libpll.a -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -/usr/bin/ranlib libwhtest.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -/usr/bin/ranlib libpll.a -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp -[ 50%] Linking CXX static library libnclextra.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -[ 50%] Built target whtest -[ 50%] Built target pll -cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -[ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp -/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o -[ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp -/usr/bin/ranlib libnclextra.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 51%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -Scanning dependencies of target pda -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 51%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp -[ 53%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp -[ 54%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp -[ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 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-msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp -[ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp -[ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp -[ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp -[ 64%] Linking CXX static library libncl.a -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 -/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -/usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 64%] Built target ncl +[ 57%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp +[ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +[ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp -[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o -[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o +[ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp +[ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp +[ 61%] Linking C static library libpll.a +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 61%] Built target pll +[ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +[ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp +[ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp +[ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp +[ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp +/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + ^~~~~ [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp -/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - ^~~~~ [ 68%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 @@ -2765,37 +2799,21 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 68%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -[ 68%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +[ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp +[ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp -[ 73%] Linking CXX static library libpda.a -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -/usr/bin/ranlib libpda.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 73%] Built target pda -[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2808,7 +2826,20 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2821,7 +2852,14 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelProtein::readRates(istream &in) throw(const char*, string) { + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2834,20 +2872,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2860,12 +2886,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2878,11 +2900,19 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: +[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -2895,15 +2925,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelProtein::readRates(istream &in) throw(const char*, string) { - ^~~~~ -[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ @@ -2916,14 +2937,27 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp +[ 76%] Linking CXX static library libpda.a +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp +cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp +/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +/usr/bin/ranlib libpda.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 77%] Built target pda [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o @@ -2931,9 +2965,11 @@ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -2948,16 +2984,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -2993,8 +3025,35 @@ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readStateFreq(istream &in) throw(const char*); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readStateFreq(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: +/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, @@ -3031,7 +3090,7 @@ /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -3044,18 +3103,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: -/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, @@ -3092,19 +3139,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readStateFreq(istream &in) throw(const char*); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readStateFreq(string str) throw(const char*); - ^~~~~ [ 84%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 @@ -3119,13 +3153,6 @@ /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target kernelsse -[ 84%] Linking CXX static library libkernelfma.a -/usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake -/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 -/usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -/usr/bin/ranlib libkernelfma.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 84%] Built target kernelfma [ 84%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 @@ -3133,6 +3160,13 @@ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target kernelavx +[ 84%] Linking CXX static library libkernelfma.a +/usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake +/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 +/usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +/usr/bin/ranlib libkernelfma.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 84%] Built target kernelfma [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -3148,36 +3182,36 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp +[ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3193,7 +3227,9 @@ virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3208,8 +3244,14 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3224,14 +3266,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } @@ -3263,21 +3297,21 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 97%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp -[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp -/build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - ^~~~~~~~ +[ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: +/build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + ^~~~~~~~ +In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -3290,19 +3324,15 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: +In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: +In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: -/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: +In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -3315,14 +3345,18 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: +In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: +In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: +/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } @@ -3338,19 +3372,19 @@ # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.mpi - cd build.mpi && make -j16 "INSTALL=install --strip-program=true" + cd build.mpi && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/mympi.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend @@ -3363,117 +3397,141 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +Scanning dependencies of target kernelfma +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= -Scanning dependencies of target gsl +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +Scanning dependencies of target kernelavx +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build Scanning dependencies of target mympi make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend -Scanning dependencies of target ncl -Scanning dependencies of target kernelavx -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -Scanning dependencies of target kernelfma -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -Scanning dependencies of target lbfgsb -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 0%] Building CXX object CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/TreeCollection.cpp -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -Scanning dependencies of target kernelsse +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +Scanning dependencies of target gsl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 1%] Building CXX object CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/ObjectStream.cpp -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +Scanning dependencies of target lbfgsb +Scanning dependencies of target kernelsse +[ 0%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +[ 0%] Building CXX object CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o Scanning dependencies of target nclextra -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp -[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp +Scanning dependencies of target pllavx +Scanning dependencies of target vectorclass +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/TreeCollection.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -[ 4%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +[ 0%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +Scanning dependencies of target sprng +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +Scanning dependencies of target whtest +Scanning dependencies of target ncl +[ 1%] Building CXX object CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/ObjectStream.cpp +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp -[ 4%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp -[ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build +[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp -[ 6%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -[ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 4%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +[ 5%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c +[ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 7%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp -[ 8%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp Scanning dependencies of target pll -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c -[ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 9%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -[ 10%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +[ 9%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +[ 10%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c +[ 10%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c -[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -[ 11%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -Scanning dependencies of target sprng +[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp +[ 11%] Linking CXX static library libvectorclass.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 12%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c -[ 13%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c -[ 13%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c +[ 11%] Built target vectorclass +[ 11%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c +[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +[ 12%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c +[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp +[ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c +In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: +/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + extern __inline unsigned int bitcount_64_bit(uint64_t i); + ^~~~~~~~~~~~~~~ +[ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c +[ 15%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c +[ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3485,12 +3543,27 @@ /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ +[ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c +[ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c +[ 18%] Linking CXX static library libgsl.a +[ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp +[ 19%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c +cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 14%] Linking CXX static library libgsl.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 19%] Linking C static library libsprng.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +[ 19%] Built target gsl In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3514,20 +3587,48 @@ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ +cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ -[ 15%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c -cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 -/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o -/usr/bin/ranlib libgsl.a +[ 20%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c +/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o +/usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 15%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c +[ 20%] Built target sprng +[ 20%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c +[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp +[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c +[ 23%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp +[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] + fscanf ( ifp, "%c", &c ); + ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 25%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c +[ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp +[ 25%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3544,53 +3645,27 @@ /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ -[ 15%] Built target gsl -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -Scanning dependencies of target vectorclass -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 15%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c -[ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Linking CXX static library libvectorclass.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 18%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c -[ 19%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +[ 26%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 19%] Built target vectorclass -In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: -/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - extern __inline unsigned int bitcount_64_bit(uint64_t i); - ^~~~~~~~~~~~~~~ -[ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp -[ 19%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +[ 26%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c -[ 19%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -[ 20%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp +[ 27%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c -[ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp +[ 28%] Linking C static library libpllavx.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] @@ -3604,43 +3679,65 @@ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ -[ 22%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -[ 23%] Building C object pll/CMakeFiles/pll.dir/models.c.o -[ 23%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 28%] Built target pllavx +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp +[ 28%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 28%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +Scanning dependencies of target utils +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 29%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp +[ 30%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c -In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp +In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 23%] Linking C static library libsprng.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp +[ 31%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c +In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o -/usr/bin/ranlib libsprng.a +[ 32%] Linking CXX static library libwhtest.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +/usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 23%] Built target sprng -[ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp -[ 25%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +[ 32%] Built target whtest +[ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp +[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp +[ 35%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c -[ 25%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c -[ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c +[ 36%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp +[ 36%] Linking CXX static library libmympi.a +/usr/bin/cmake -P CMakeFiles/mympi.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: -/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - extern __inline unsigned int bitcount_64_bit(uint64_t i); - ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] @@ -3653,6 +3750,9 @@ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ +/usr/bin/cmake -E cmake_link_script CMakeFiles/mympi.dir/link.txt --verbose=1 +[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign @@ -3665,150 +3765,100 @@ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c -[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c -[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp -[ 29%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +/usr/bin/ar qc libmympi.a CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o +/usr/bin/ranlib libmympi.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 36%] Built target mympi +[ 36%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp +In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: +/build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + extern __inline unsigned int bitcount_64_bit(uint64_t i); + ^~~~~~~~~~~~~~~ +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp +[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp +[ 39%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c -[ 29%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ +[ 39%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp +[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp +[ 40%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp +[ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp +[ 41%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c -[ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] - fscanf ( ifp, "%c", &c ); - ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -[ 30%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +[ 42%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp +[ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp -[ 30%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +[ 43%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c +[ 44%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c +[ 45%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 30%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 31%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c -[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp -[ 32%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 32%] Linking C static library libpllavx.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +[ 45%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -Scanning dependencies of target utils -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 33%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 34%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -[ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c -[ 35%] Built target pllavx -[ 35%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp +[ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 35%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c -[ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp +[ 46%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 36%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -[ 36%] Linking CXX static library libmympi.a -/usr/bin/cmake -P CMakeFiles/mympi.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp -/usr/bin/cmake -E cmake_link_script CMakeFiles/mympi.dir/link.txt --verbose=1 -/usr/bin/ar qc libmympi.a CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o -/usr/bin/ranlib libmympi.a -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 36%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c -[ 36%] Built target mympi -[ 37%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp -[ 37%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp -[ 38%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp -[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp -[ 40%] Linking CXX static library libwhtest.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -[ 40%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -/usr/bin/ranlib libwhtest.a +[ 47%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 41%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c -[ 41%] Built target whtest -[ 42%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c -In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: +In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 43%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp -In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: +[ 48%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c +[ 49%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c +In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ -[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -[ 45%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3871,23 +3921,15 @@ /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp -[ 46%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp -[ 48%] Linking CXX static library libnclextra.a +[ 51%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a -[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 49%] Built target nclextra +[ 51%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= @@ -3895,58 +3937,32 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp -[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp -[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp -[ 50%] Linking C static library libpll.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 -/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o -[ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -/usr/bin/ranlib libpll.a -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 51%] Built target pll -[ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp +[ 54%] Linking C static library libpll.a +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 +/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 54%] Built target pll [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include 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CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp -[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp +[ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp +/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { + ^~~~~ [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp -/build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { - ^~~~~ [ 63%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 @@ -3987,22 +4021,24 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp -[ 65%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +[ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp -[ 65%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp -[ 66%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp -[ 66%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +[ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp +[ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: +[ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp +[ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4015,15 +4051,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - void ModelProtein::readRates(istream &in) throw(const char*, string) { - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4036,16 +4069,10 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ -[ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4058,8 +4085,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4072,20 +4099,15 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: -/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: +In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, - from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: +/build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + void ModelProtein::readRates(istream &in) throw(const char*, string) { + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4098,11 +4120,7 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp -In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4115,8 +4133,22 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 70%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +[ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp [ 71%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 @@ -4124,26 +4156,28 @@ /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 71%] Built target pda +[ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ -[ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ +[ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp +[ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o @@ -4154,6 +4188,8 @@ cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp +[ 77%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4168,16 +4204,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -[ 77%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp -[ 78%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp -[ 78%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4192,6 +4220,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +[ 78%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp +[ 78%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp +[ 79%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4213,20 +4247,9 @@ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, - from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(istream &in) throw(const char*, string); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readRates(string str) throw(const char*); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readStateFreq(istream &in) throw(const char*); - ^~~~~ -/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - virtual void readStateFreq(string str) throw(const char*); - ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -4240,6 +4263,7 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); @@ -4252,13 +4276,24 @@ /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp +In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, + from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(istream &in) throw(const char*, string); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readRates(string str) throw(const char*); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readStateFreq(istream &in) throw(const char*); + ^~~~~ +/build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + virtual void readStateFreq(string str) throw(const char*); + ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4272,14 +4307,14 @@ virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: + from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4293,13 +4328,11 @@ virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: + from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, - from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: +In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4312,7 +4345,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: +In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, + from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ @@ -4367,38 +4401,36 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -4412,6 +4444,8 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, @@ -4450,12 +4484,6 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ -/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] - } - ^ -[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); @@ -4469,6 +4497,12 @@ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ +[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp +/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] + } + ^ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -4483,14 +4517,14 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o -[ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ @@ -4566,18 +4600,18 @@ echo 'time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo' >> example.short time sh example.short Executing tests using /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp ... -+ time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy ++ /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos5-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -Seed: 215912 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Fri Aug 5 07:42:21 2022 -Kernel: AVX - 1 threads (16 CPU cores detected) +Seed: 652437 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Sun Jul 4 03:38:31 2021 +Kernel: AVX - 1 threads (15 CPU cores detected) -HINT: Use -nt option to specify number of threads because your CPU has 16 cores! +HINT: Use -nt option to specify number of threads because your CPU has 15 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected @@ -4632,270 +4666,274 @@ **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) -Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC - 1 JC 11923.628 85 24017.255 24066.316 24353.060 - 2 JC+I 11669.883 86 23511.767 23562.150 23851.522 - 3 JC+G4 11363.296 86 22898.591 22948.975 23238.346 - 4 JC+I+G4 11346.433 87 22866.867 22918.597 23210.573 - 5 JC+R2 11460.283 87 23094.567 23146.297 23438.273 - 6 JC+R3 11349.557 89 22877.115 22931.605 23228.722 - 7 JC+R4 11340.087 91 22862.174 22919.516 23221.682 - 8 JC+R5 11339.948 93 22865.897 22926.187 23233.307 - 14 F81+F 11927.333 88 24030.666 24083.765 24378.323 - 15 F81+F+I 11670.259 89 23518.518 23573.008 23870.125 - 16 F81+F+G4 11358.529 89 22895.058 22949.547 23246.665 - 17 F81+F+I+G4 11341.895 90 22863.789 22919.694 23219.347 - 18 F81+F+R2 11457.886 90 23095.773 23151.677 23451.331 - 19 F81+F+R3 11345.804 92 22875.608 22934.412 23239.067 - 20 F81+F+R4 11335.393 94 22858.786 22920.585 23230.146 - 21 F81+F+R5 11335.282 96 22862.564 22927.455 23241.825 - 27 K2P 11881.076 86 23934.153 23984.537 24273.908 - 28 K2P+I 11627.075 87 23428.149 23479.879 23771.855 - 29 K2P+G4 11316.740 87 22807.480 22859.210 23151.186 - 30 K2P+I+G4 11300.267 88 22776.533 22829.632 23124.190 - 31 K2P+R2 11416.205 88 23008.409 23061.508 23356.066 - 32 K2P+R3 11303.971 90 22787.942 22843.846 23143.500 - 33 K2P+R4 11293.768 92 22771.536 22830.340 23134.995 - 34 K2P+R5 11293.664 94 22775.327 22837.127 23146.688 - 40 HKY+F 11884.045 89 23946.090 24000.580 24297.697 - 41 HKY+F+I 11625.800 90 23431.599 23487.503 23787.157 - 42 HKY+F+G4 11309.303 90 22798.605 22854.510 23154.163 - 43 HKY+F+I+G4 11293.017 91 22768.033 22825.376 23127.542 - 44 HKY+F+R2 11411.536 91 23005.072 23062.415 23364.581 - 45 HKY+F+R3 11297.610 93 22781.221 22841.510 23148.630 - 46 HKY+F+R4 11286.412 95 22762.823 22826.157 23138.134 - 47 HKY+F+R5 11286.351 97 22766.702 22833.178 23149.915 - 53 TNe 11880.065 87 23934.130 23985.859 24277.835 - 54 TNe+I 11620.650 88 23417.300 23470.398 23764.956 - 55 TNe+G4 11315.459 88 22806.918 22860.016 23154.575 - 56 TNe+I+G4 11298.288 89 22774.575 22829.065 23126.182 - 57 TNe+R2 11414.812 89 23007.624 23062.114 23359.232 - 58 TNe+R3 11300.588 91 22783.175 22840.518 23142.684 - 59 TNe+R4 11290.964 93 22767.928 22828.218 23135.338 - 60 TNe+R5 11290.801 95 22771.601 22834.935 23146.912 - 66 TN+F 11882.917 90 23945.834 24001.739 24301.392 - 67 TN+F+I 11618.509 91 23419.019 23476.361 23778.527 - 68 TN+F+G4 11307.383 91 22796.766 22854.108 23156.274 - 69 TN+F+I+G4 11290.263 92 22764.527 22823.331 23127.986 - 70 TN+F+R2 11409.606 92 23003.211 23062.015 23366.670 - 71 TN+F+R3 11293.299 94 22774.598 22836.398 23145.959 - 72 TN+F+R4 11282.625 96 22757.250 22822.142 23136.512 - 73 TN+F+R5 11282.545 98 22761.089 22829.174 23148.252 - 79 K3P 11867.490 87 23908.981 23960.711 24252.687 - 80 K3P+I 11612.745 88 23401.490 23454.588 23749.146 - 81 K3P+G4 11305.537 88 22787.073 22840.172 23134.730 - 82 K3P+I+G4 11288.477 89 22754.954 22809.444 23106.561 - 83 K3P+R2 11401.945 89 22981.891 23036.381 23333.498 - 84 K3P+R3 11291.942 91 22765.885 22823.227 23125.393 - 85 K3P+R4 11282.100 93 22750.200 22810.490 23117.610 - 86 K3P+R5 11282.046 95 22754.092 22817.426 23129.403 - 92 K3Pu+F 11870.569 90 23921.138 23977.043 24276.696 - 93 K3Pu+F+I 11611.617 91 23405.233 23462.576 23764.742 - 94 K3Pu+F+G4 11298.775 91 22779.549 22836.892 23139.058 - 95 K3Pu+F+I+G4 11281.879 92 22747.758 22806.562 23111.217 - 96 K3Pu+F+R2 11397.646 92 22979.292 23038.096 23342.751 - 97 K3Pu+F+R3 11286.226 94 22760.452 22822.251 23131.812 - 98 K3Pu+F+R4 11275.375 96 22742.751 22807.643 23122.013 - 99 K3Pu+F+R5 11275.327 98 22746.654 22814.738 23133.817 -105 TPM2+F 11883.629 90 23947.257 24003.162 24302.815 -106 TPM2+F+I 11625.200 91 23432.400 23489.742 23791.908 -107 TPM2+F+G4 11308.868 91 22799.735 22857.078 23159.244 -108 TPM2+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 -109 TPM2+F+R2 11411.526 92 23007.053 23065.857 23370.512 -110 TPM2+F+R3 11297.355 94 22782.711 22844.510 23154.071 -111 TPM2+F+R4 11286.270 96 22764.539 22829.431 23143.801 -112 TPM2+F+R5 11286.146 98 22768.292 22836.376 23155.455 -118 TPM2u+F 11883.629 90 23947.258 24003.162 24302.815 -119 TPM2u+F+I 11625.201 91 23432.402 23489.745 23791.911 -120 TPM2u+F+G4 11308.867 91 22799.735 22857.077 23159.243 -121 TPM2u+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 -122 TPM2u+F+R2 11411.527 92 23007.053 23065.857 23370.512 -123 TPM2u+F+R3 11297.355 94 22782.710 22844.509 23154.070 -124 TPM2u+F+R4 11286.270 96 22764.540 22829.432 23143.802 -125 TPM2u+F+R5 11286.143 98 22768.285 22836.370 23155.448 -131 TPM3+F 11851.525 90 23883.050 23938.954 24238.608 -132 TPM3+F+I 11613.469 91 23408.938 23466.281 23768.447 -133 TPM3+F+G4 11305.327 91 22792.654 22849.996 23152.162 -134 TPM3+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 -135 TPM3+F+R2 11405.175 92 22994.351 23053.155 23357.810 -136 TPM3+F+R3 11293.007 94 22774.014 22835.813 23145.374 -137 TPM3+F+R4 11283.178 96 22758.356 22823.248 23137.618 -138 TPM3+F+R5 11283.049 98 22762.099 22830.183 23149.262 -144 TPM3u+F 11851.525 90 23883.050 23938.954 24238.608 -145 TPM3u+F+I 11613.469 91 23408.938 23466.281 23768.447 -146 TPM3u+F+G4 11305.327 91 22792.655 22849.997 23152.163 -147 TPM3u+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 -148 TPM3u+F+R2 11405.172 92 22994.345 23053.149 23357.804 -149 TPM3u+F+R3 11293.007 94 22774.014 22835.813 23145.374 -150 TPM3u+F+R4 11283.172 96 22758.344 22823.236 23137.606 -151 TPM3u+F+R5 11283.047 98 22762.095 22830.179 23149.258 -157 TIMe 11866.486 88 23908.972 23962.070 24256.629 -158 TIMe+I 11606.350 89 23390.699 23445.189 23742.306 -159 TIMe+G4 11304.322 89 22786.643 22841.133 23138.250 -160 TIMe+I+G4 11286.570 90 22753.139 22809.044 23108.697 -161 TIMe+R2 11400.580 90 22981.161 23037.065 23336.718 -162 TIMe+R3 11288.530 92 22761.060 22819.864 23124.519 -163 TIMe+R4 11279.399 94 22746.797 22808.596 23118.158 -164 TIMe+R5 11279.309 96 22750.619 22815.511 23129.880 -170 TIM+F 11869.451 91 23920.901 23978.244 24280.410 -171 TIM+F+I 11604.362 92 23392.723 23451.527 23756.182 -172 TIM+F+G4 11296.948 92 22777.895 22836.699 23141.354 -173 TIM+F+I+G4 11279.221 93 22744.442 22804.732 23111.852 -174 TIM+F+R2 11395.723 93 22977.446 23037.735 23344.855 -175 TIM+F+R3 11281.905 95 22753.810 22817.144 23129.121 -176 TIM+F+R4 11271.730 97 22737.460 22803.935 23120.672 -177 TIM+F+R5 11271.695 99 22741.389 22811.107 23132.503 -183 TIM2e 11879.551 88 23935.102 23988.200 24282.758 -184 TIM2e+I 11619.949 89 23417.898 23472.388 23769.506 -185 TIM2e+G4 11315.204 89 22808.409 22862.898 23160.016 -186 TIM2e+I+G4 11298.141 90 22776.282 22832.187 23131.840 -187 TIM2e+R2 11414.742 90 23009.484 23065.388 23365.041 -188 TIM2e+R3 11300.473 92 22784.945 22843.750 23148.405 -189 TIM2e+R4 11290.833 94 22769.667 22831.466 23141.027 -190 TIM2e+R5 11290.739 96 22773.478 22838.370 23152.740 -196 TIM2+F 11882.506 91 23947.012 24004.354 24306.520 -197 TIM2+F+I 11617.928 92 23419.855 23478.659 23783.314 -198 TIM2+F+G4 11306.963 92 22797.925 22856.729 23161.384 -199 TIM2+F+I+G4 11289.986 93 22765.972 22826.262 23133.382 -200 TIM2+F+R2 11409.581 93 23005.161 23065.451 23372.571 -201 TIM2+F+R3 11293.076 95 22776.151 22839.485 23151.462 -202 TIM2+F+R4 11282.473 97 22758.946 22825.422 23142.159 -203 TIM2+F+R5 11282.402 99 22762.805 22832.523 23153.918 -209 TIM3e 11838.747 88 23853.494 23906.592 24201.150 -210 TIM3e+I 11602.540 89 23383.080 23437.570 23734.687 -211 TIM3e+G4 11307.306 89 22792.612 22847.102 23144.219 -212 TIM3e+I+G4 11291.340 90 22762.680 22818.585 23118.238 -213 TIM3e+R2 11403.257 90 22986.513 23042.418 23342.071 -214 TIM3e+R3 11291.597 92 22767.193 22825.997 23130.652 -215 TIM3e+R4 11283.522 94 22755.045 22816.844 23126.405 -216 TIM3e+R5 11283.418 96 22758.835 22823.727 23138.097 -222 TIM3+F 11850.147 91 23882.293 23939.636 24241.802 -223 TIM3+F+I 11606.170 92 23396.339 23455.144 23759.799 -224 TIM3+F+G4 11303.297 92 22790.593 22849.397 23154.052 -225 TIM3+F+I+G4 11287.023 93 22760.046 22820.336 23127.456 -226 TIM3+F+R2 11403.216 93 22992.433 23052.722 23359.842 -227 TIM3+F+R3 11288.650 95 22767.299 22830.632 23142.610 -228 TIM3+F+R4 11279.141 97 22752.282 22818.757 23135.494 -229 TIM3+F+R5 11279.094 99 22756.187 22825.905 23147.301 -235 TVMe 11826.121 89 23830.242 23884.732 24181.849 -236 TVMe+I 11594.361 90 23368.722 23424.627 23724.280 -237 TVMe+G4 11295.606 90 22771.211 22827.116 23126.769 -238 TVMe+I+G4 11280.065 91 22742.130 22799.473 23101.639 -239 TVMe+R2 11390.331 91 22962.661 23020.004 23322.170 -240 TVMe+R3 11281.356 93 22748.713 22809.003 23116.123 -241 TVMe+R4 11273.798 95 22737.595 22800.929 23112.906 -242 TVMe+R5 11273.698 97 22741.396 22807.871 23124.608 -248 TVM+F 11837.769 92 23859.537 23918.341 24222.996 -249 TVM+F+I 11599.049 93 23384.097 23444.387 23751.507 -250 TVM+F+G4 11292.632 93 22771.264 22831.554 23138.674 -251 TVM+F+I+G4 11276.861 94 22741.721 22803.521 23113.082 -252 TVM+F+R2 11390.890 94 22969.780 23031.579 23341.140 -253 TVM+F+R3 11279.704 96 22751.409 22816.301 23130.671 -254 TVM+F+R4 11270.720 98 22737.439 22805.524 23124.602 -255 TVM+F+R5 11270.590 100 22741.181 22812.559 23136.245 -261 SYM 11824.854 90 23829.707 23885.612 24185.265 -262 SYM+I 11587.951 91 23357.902 23415.245 23717.411 -263 SYM+G4 11294.178 91 22770.357 22827.699 23129.865 -264 SYM+I+G4 11278.013 92 22740.027 22798.831 23103.486 -265 SYM+R2 11388.873 92 22961.746 23020.550 23325.205 -266 SYM+R3 11277.825 94 22743.649 22805.449 23115.010 -267 SYM+R4 11270.756 96 22733.511 22798.403 23112.773 -268 SYM+R5 11270.608 98 22737.216 22805.300 23124.379 -274 GTR+F 11836.396 93 23858.792 23919.082 24226.202 -275 GTR+F+I 11591.768 94 23371.536 23433.336 23742.897 -276 GTR+F+G4 11290.699 94 22769.397 22831.197 23140.758 -277 GTR+F+I+G4 11274.183 95 22738.365 22801.698 23113.676 -278 GTR+F+R2 11389.047 95 22968.093 23031.427 23343.404 -279 GTR+F+R3 11275.377 97 22744.753 22811.229 23127.966 -280 GTR+F+R4 11266.912 99 22731.824 22801.543 23122.938 -281 GTR+F+R5 11266.818 101 22735.637 22808.701 23134.652 + 1 JC 12015.193 85 24200.386 24249.447 24536.191 + 2 JC+I 11749.817 86 23671.635 23722.019 24011.390 + 3 JC+G4 11426.892 86 23025.785 23076.169 23365.540 + 4 JC+I+G4 11409.860 87 22993.720 23045.450 23337.426 + 5 JC+R2 11538.548 87 23251.096 23302.826 23594.802 + 6 JC+R3 11416.865 89 23011.730 23066.220 23363.337 + 7 JC+R4 11408.567 91 22999.135 23056.477 23358.643 + 8 JC+R5 11407.459 93 23000.917 23061.207 23368.327 + 14 F81+F 12014.723 88 24205.447 24258.545 24553.103 + 15 F81+F+I 11746.066 89 23670.131 23724.621 24021.738 + 16 F81+F+G4 11418.644 89 23015.289 23069.779 23366.896 + 17 F81+F+I+G4 11401.906 90 22983.812 23039.716 23339.370 + 18 F81+F+R2 11532.431 90 23244.861 23300.766 23600.419 + 19 F81+F+R3 11409.624 92 23003.248 23062.052 23366.707 + 20 F81+F+R4 11399.419 94 22986.839 23048.638 23358.199 + 21 F81+F+R5 11399.287 96 22990.575 23055.467 23369.836 + 27 K2P 11970.818 86 24113.636 24164.020 24453.391 + 28 K2P+I 11705.384 87 23584.767 23636.497 23928.473 + 29 K2P+G4 11377.365 87 22928.730 22980.460 23272.436 + 30 K2P+I+G4 11360.860 88 22897.720 22950.818 23245.377 + 31 K2P+R2 11491.642 88 23159.283 23212.382 23506.940 + 32 K2P+R3 11368.396 90 22916.792 22972.696 23272.350 + 33 K2P+R4 11358.063 92 22900.125 22958.930 23263.584 + 34 K2P+R5 11358.037 94 22904.074 22965.874 23275.435 + 40 HKY+F 11969.910 89 24117.819 24172.309 24469.426 + 41 HKY+F+I 11700.293 90 23580.586 23636.490 23936.144 + 42 HKY+F+G4 11366.737 90 22913.475 22969.379 23269.032 + 43 HKY+F+I+G4 11350.329 91 22882.659 22940.001 23242.167 + 44 HKY+F+R2 11483.520 91 23149.039 23206.382 23508.548 + 45 HKY+F+R3 11358.705 93 22903.410 22963.700 23270.820 + 46 HKY+F+R4 11347.352 95 22884.703 22948.037 23260.014 + 47 HKY+F+R5 11347.339 97 22888.678 22955.154 23271.891 + 53 TNe 11969.088 87 24112.176 24163.906 24455.882 + 54 TNe+I 11696.852 88 23569.705 23622.803 23917.361 + 55 TNe+G4 11374.378 88 22924.756 22977.854 23272.412 + 56 TNe+I+G4 11357.169 89 22892.337 22946.827 23243.945 + 57 TNe+R2 11489.369 89 23156.738 23211.228 23508.345 + 58 TNe+R3 11362.661 91 22907.323 22964.665 23266.831 + 59 TNe+R4 11353.344 93 22892.689 22952.978 23260.098 + 60 TNe+R5 11353.332 95 22896.664 22959.997 23271.975 + 66 TN+F 11968.110 90 24116.221 24172.125 24471.779 + 67 TN+F+I 11690.996 91 23563.992 23621.335 23923.501 + 68 TN+F+G4 11362.959 91 22907.919 22965.261 23267.427 + 69 TN+F+I+G4 11345.763 92 22875.526 22934.330 23238.985 + 70 TN+F+R2 11480.714 92 23145.429 23204.233 23508.888 + 71 TN+F+R3 11351.854 94 22891.708 22953.507 23263.068 + 72 TN+F+R4 11341.711 96 22875.421 22940.313 23254.683 + 73 TN+F+R5 11341.613 98 22879.227 22947.311 23266.390 + 79 K3P 11955.726 87 24085.452 24137.182 24429.158 + 80 K3P+I 11689.786 88 23555.572 23608.670 23903.229 + 81 K3P+G4 11366.551 88 22909.101 22962.200 23256.758 + 82 K3P+I+G4 11349.411 89 22876.821 22931.311 23228.429 + 83 K3P+R2 11477.146 89 23132.292 23186.782 23483.899 + 84 K3P+R3 11357.300 91 22896.599 22953.942 23256.108 + 85 K3P+R4 11346.132 93 22878.264 22938.554 23245.674 + 86 K3P+R5 11346.075 95 22882.150 22945.483 23257.461 + 92 K3Pu+F 11954.797 90 24089.594 24145.498 24445.152 + 93 K3Pu+F+I 11684.711 91 23551.421 23608.764 23910.930 + 94 K3Pu+F+G4 11356.428 91 22894.856 22952.198 23254.364 + 95 K3Pu+F+I+G4 11339.416 92 22862.833 22921.637 23226.292 + 96 K3Pu+F+R2 11469.398 92 23122.796 23181.600 23486.255 + 97 K3Pu+F+R3 11348.095 94 22884.191 22945.990 23255.551 + 98 K3Pu+F+R4 11335.892 96 22863.784 22928.676 23243.046 + 99 K3Pu+F+R5 11335.816 98 22867.632 22935.716 23254.795 +105 TPM2+F 11969.902 90 24119.804 24175.708 24475.361 +106 TPM2+F+I 11700.222 91 23582.444 23639.787 23941.953 +107 TPM2+F+G4 11365.880 91 22913.760 22971.103 23273.269 +108 TPM2+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 +109 TPM2+F+R2 11483.376 92 23150.752 23209.556 23514.211 +110 TPM2+F+R3 11358.087 94 22904.173 22965.972 23275.533 +111 TPM2+F+R4 11346.136 96 22884.272 22949.164 23263.533 +112 TPM2+F+R5 11346.063 98 22888.126 22956.210 23275.289 +118 TPM2u+F 11969.903 90 24119.805 24175.710 24475.363 +119 TPM2u+F+I 11700.223 91 23582.445 23639.788 23941.954 +120 TPM2u+F+G4 11365.880 91 22913.760 22971.102 23273.268 +121 TPM2u+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 +122 TPM2u+F+R2 11483.380 92 23150.760 23209.564 23514.219 +123 TPM2u+F+R3 11358.086 94 22904.173 22965.972 23275.533 +124 TPM2u+F+R4 11346.012 96 22884.023 22948.915 23263.285 +125 TPM2u+F+R5 11346.004 98 22888.009 22956.093 23275.172 +131 TPM3+F 11939.208 90 24058.415 24114.320 24413.973 +132 TPM3+F+I 11688.861 91 23559.723 23617.065 23919.231 +133 TPM3+F+G4 11362.780 91 22907.560 22964.903 23267.069 +134 TPM3+F+I+G4 11347.020 92 22878.039 22936.843 23241.498 +135 TPM3+F+R2 11476.513 92 23137.026 23195.830 23500.485 +136 TPM3+F+R3 11353.918 94 22895.835 22957.634 23267.196 +137 TPM3+F+R4 11342.967 96 22877.935 22942.827 23257.196 +138 TPM3+F+R5 11342.922 98 22881.844 22949.928 23269.007 +144 TPM3u+F 11939.209 90 24058.418 24114.323 24413.976 +145 TPM3u+F+I 11688.862 91 23559.723 23617.066 23919.232 +146 TPM3u+F+G4 11362.781 91 22907.561 22964.904 23267.070 +147 TPM3u+F+I+G4 11347.020 92 22878.040 22936.844 23241.499 +148 TPM3u+F+R2 11476.515 92 23137.030 23195.834 23500.489 +149 TPM3u+F+R3 11353.918 94 22895.835 22957.634 23267.195 +150 TPM3u+F+R4 11342.887 96 22877.774 22942.666 23257.036 +151 TPM3u+F+R5 11342.887 98 22881.774 22949.858 23268.937 +157 TIMe 11954.065 88 24084.129 24137.228 24431.786 +158 TIMe+I 11681.462 89 23540.924 23595.413 23892.531 +159 TIMe+G4 11363.653 89 22905.306 22959.796 23256.913 +160 TIMe+I+G4 11345.802 90 22871.603 22927.508 23227.161 +161 TIMe+R2 11475.095 90 23130.189 23186.094 23485.747 +162 TIMe+R3 11351.551 92 22887.101 22945.905 23250.560 +163 TIMe+R4 11341.268 94 22870.536 22932.335 23241.896 +164 TIMe+R5 11341.264 96 22874.528 22939.420 23253.790 +170 TIM+F 11953.073 91 24088.145 24145.488 24447.654 +171 TIM+F+I 11675.638 92 23535.276 23594.080 23898.735 +172 TIM+F+G4 11352.739 92 22889.478 22948.282 23252.937 +173 TIM+F+I+G4 11334.933 93 22855.867 22916.156 23223.276 +174 TIM+F+R2 11466.803 93 23119.606 23179.896 23487.016 +175 TIM+F+R3 11341.217 95 22872.434 22935.768 23247.745 +176 TIM+F+R4 11330.083 97 22854.165 22920.641 23237.378 +177 TIM+F+R5 11330.040 99 22858.080 22927.799 23249.194 +183 TIM2e 11969.060 88 24114.119 24167.218 24461.776 +184 TIM2e+I 11696.724 89 23571.449 23625.939 23923.056 +185 TIM2e+G4 11373.751 89 22925.503 22979.993 23277.110 +186 TIM2e+I+G4 11356.625 90 22893.250 22949.154 23248.808 +187 TIM2e+R2 11489.326 90 23158.651 23214.556 23514.209 +188 TIM2e+R3 11362.313 92 22908.626 22967.431 23272.086 +189 TIM2e+R4 11352.064 94 22892.128 22953.927 23263.488 +190 TIM2e+R5 11352.061 96 22896.122 22961.014 23275.384 +196 TIM2+F 11968.103 91 24118.206 24175.549 24477.715 +197 TIM2+F+I 11690.924 92 23565.848 23624.653 23929.308 +198 TIM2+F+G4 11362.111 92 22908.222 22967.027 23271.682 +199 TIM2+F+I+G4 11345.003 93 22876.007 22936.297 23243.417 +200 TIM2+F+R2 11480.623 93 23147.246 23207.536 23514.656 +201 TIM2+F+R3 11351.348 95 22892.696 22956.029 23268.007 +202 TIM2+F+R4 11340.298 97 22874.597 22941.072 23257.809 +203 TIM2+F+R5 11340.262 99 22878.523 22948.242 23269.637 +209 TIM3e 11929.583 88 24035.165 24088.263 24382.822 +210 TIM3e+I 11679.665 89 23537.329 23591.819 23888.937 +211 TIM3e+G4 11366.249 89 22910.499 22964.989 23262.106 +212 TIM3e+I+G4 11350.100 90 22880.199 22936.104 23235.757 +213 TIM3e+R2 11477.347 90 23134.694 23190.598 23490.252 +214 TIM3e+R3 11353.723 92 22891.445 22950.249 23254.904 +215 TIM3e+R4 11345.129 94 22878.259 22940.058 23249.619 +216 TIM3e+R5 11345.116 96 22882.233 22947.125 23261.494 +222 TIM3+F 11937.046 91 24056.091 24113.433 24415.599 +223 TIM3+F+I 11679.411 92 23542.822 23601.627 23906.282 +224 TIM3+F+G4 11358.813 92 22901.625 22960.429 23265.084 +225 TIM3+F+I+G4 11342.334 93 22870.668 22930.957 23238.077 +226 TIM3+F+R2 11473.687 93 23133.374 23193.664 23500.784 +227 TIM3+F+R3 11347.077 95 22884.154 22947.488 23259.465 +228 TIM3+F+R4 11337.180 97 22868.361 22934.836 23251.573 +229 TIM3+F+R5 11337.160 99 22872.319 22942.037 23263.433 +235 TVMe 11915.914 89 24009.828 24064.317 24361.435 +236 TVMe+I 11672.235 90 23524.469 23580.374 23880.027 +237 TVMe+G4 11355.962 90 22891.924 22947.828 23247.481 +238 TVMe+I+G4 11340.052 91 22862.103 22919.446 23221.612 +239 TVMe+R2 11464.332 91 23110.664 23168.006 23470.172 +240 TVMe+R3 11345.869 93 22877.738 22938.028 23245.148 +241 TVMe+R4 11336.465 95 22862.930 22926.264 23238.241 +242 TVMe+R5 11336.449 97 22866.898 22933.374 23250.111 +248 TVM+F 11923.307 92 24030.614 24089.418 24394.073 +249 TVM+F+I 11672.689 93 23531.379 23591.668 23898.789 +250 TVM+F+G4 11349.481 93 22884.961 22945.251 23252.371 +251 TVM+F+I+G4 11333.273 94 22854.547 22916.346 23225.907 +252 TVM+F+R2 11461.206 94 23110.412 23172.211 23481.772 +253 TVM+F+R3 11340.584 96 22873.169 22938.061 23252.431 +254 TVM+F+R4 11329.650 98 22855.299 22923.383 23242.462 +255 TVM+F+R5 11329.621 100 22859.241 22930.619 23254.305 +261 SYM 11913.886 90 24007.771 24063.676 24363.329 +262 SYM+I 11663.801 91 23509.602 23566.945 23869.111 +263 SYM+G4 11352.816 91 22887.633 22944.975 23247.141 +264 SYM+I+G4 11336.290 92 22856.581 22915.385 23220.040 +265 SYM+R2 11462.111 92 23108.223 23167.027 23471.682 +266 SYM+R3 11340.196 94 22868.392 22930.192 23239.753 +267 SYM+R4 11332.021 96 22856.043 22920.935 23235.305 +268 SYM+R5 11332.007 98 22860.014 22928.098 23247.177 +274 GTR+F 11921.235 93 24028.470 24088.759 24395.880 +275 GTR+F+I 11663.491 94 23514.983 23576.782 23886.343 +276 GTR+F+G4 11345.623 94 22879.246 22941.045 23250.606 +277 GTR+F+I+G4 11328.789 95 22847.578 22910.912 23222.890 +278 GTR+F+R2 11458.594 95 23107.189 23170.522 23482.500 +279 GTR+F+R3 11333.883 97 22861.767 22928.242 23244.979 +280 GTR+F+R4 11324.370 99 22846.739 22916.457 23237.853 +281 GTR+F+R5 11324.349 101 22850.699 22923.762 23249.713 Akaike Information Criterion: GTR+F+R4 -Corrected Akaike Information Criterion: SYM+R4 -Bayesian Information Criterion: TVMe+I+G4 -Best-fit model: TVMe+I+G4 chosen according to BIC +Corrected Akaike Information Criterion: GTR+F+I+G4 +Bayesian Information Criterion: SYM+I+G4 +Best-fit model: SYM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 33.140 seconds (0h:0m:33s) -Wall-clock time for ModelFinder: 34.616 seconds (0h:0m:34s) +CPU time for ModelFinder: 44.294 seconds (0h:0m:44s) +Wall-clock time for ModelFinder: 66.960 seconds (0h:1m:6s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... -Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.955 / LogL: -11295.603 -Init pinv, alpha: 0.012, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.077 -Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.570 / LogL: -11280.070 -Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.568 / LogL: -11280.070 -Init pinv, alpha: 0.046, 1.000 / Estimate: 0.085, 1.571 / LogL: -11280.067 -Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.569 / LogL: -11280.068 -Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.065 -Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.575 / LogL: -11280.064 -Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.064 -Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.065 -Optimal pinv,alpha: 0.085, 1.575 / LogL: -11280.064 +Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.872 / LogL: -11352.830 +Init pinv, alpha: 0.012, 1.000 / Estimate: 0.086, 1.479 / LogL: -11336.284 +Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.484 / LogL: -11336.280 +Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 +Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.486 / LogL: -11336.278 +Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 +Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.485 / LogL: -11336.279 +Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.487 / LogL: -11336.278 +Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.488 / LogL: -11336.278 +Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.490 / LogL: -11336.278 +Optimal pinv,alpha: 0.087, 1.488 / LogL: -11336.278 -Parameters optimization took 3.767 sec -Computing ML distances based on estimated model parameters... 0.021 sec +Parameters optimization took 4.570 sec +Computing ML distances based on estimated model parameters... 0.028 sec Computing BIONJ tree... -0.001 seconds -Log-likelihood of BIONJ tree: -11256.375 +0.003 seconds +Log-likelihood of BIONJ tree: -11256.524 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 0.895 second -Computing log-likelihood of 98 initial trees ... 4.293 seconds -Current best score: -11233.108 +Generating 98 parsimony trees... 1.788 second +Computing log-likelihood of 98 initial trees ... 5.003 seconds +Current best score: -11232.454 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11225.475 -Iteration 10 / LogL: -11232.108 / Time: 0h:0m:12s -Iteration 20 / LogL: -11225.691 / Time: 0h:0m:16s -Finish initializing candidate tree set (14) -Current best tree score: -11225.475 / CPU time: 12.229 +BETTER TREE FOUND at iteration 1: -11229.757 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 2: -11224.589 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 4: -11222.746 +Iteration 10 / LogL: -11224.681 / Time: 0h:0m:16s +Iteration 20 / LogL: -11224.683 / Time: 0h:0m:19s +Finish initializing candidate tree set (13) +Current best tree score: -11222.746 / CPU time: 15.000 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- +Iteration 30 / LogL: -11223.099 / Time: 0h:0m:24s (0h:1m:3s left) +Iteration 40 / LogL: -11222.967 / Time: 0h:0m:31s (0h:0m:50s left) +Iteration 50 / LogL: -11223.103 / Time: 0h:0m:39s (0h:0m:43s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 22: -11224.924 -Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 29: -11224.866 -Iteration 30 / LogL: -11224.955 / Time: 0h:0m:21s (0h:1m:13s left) -Iteration 40 / LogL: -11224.966 / Time: 0h:0m:27s (0h:1m:1s left) -Iteration 50 / LogL: -11228.751 / Time: 0h:0m:33s (0h:0m:53s left) -Iteration 60 / LogL: -11228.617 / Time: 0h:0m:38s (0h:0m:44s left) -Iteration 70 / LogL: -11225.586 / Time: 0h:0m:42s (0h:0m:36s left) -Iteration 80 / LogL: -11228.548 / Time: 0h:0m:47s (0h:0m:29s left) -Iteration 90 / LogL: -11225.538 / Time: 0h:0m:51s (0h:0m:22s left) -Iteration 100 / LogL: -11225.072 / Time: 0h:0m:55s (0h:0m:16s left) -Iteration 110 / LogL: -11225.606 / Time: 0h:0m:59s (0h:0m:10s left) -Iteration 120 / LogL: -11228.525 / Time: 0h:1m:3s (0h:0m:4s left) -Iteration 130 / LogL: -11225.578 / Time: 0h:1m:7s (0h:0m:-1s left) -TREE SEARCH COMPLETED AFTER 130 ITERATIONS / Time: 0h:1m:7s +BETTER TREE FOUND at iteration 58: -11222.586 +Iteration 60 / LogL: -11222.964 / Time: 0h:0m:45s (0h:1m:15s left) +Iteration 70 / LogL: -11222.613 / Time: 0h:0m:49s (0h:1m:3s left) +Iteration 80 / LogL: -11222.617 / Time: 0h:0m:54s (0h:0m:53s left) +Iteration 90 / LogL: -11222.729 / Time: 0h:1m:1s (0h:0m:47s left) +Iteration 100 / LogL: -11222.896 / Time: 0h:1m:5s (0h:0m:38s left) +Iteration 110 / LogL: -11222.658 / Time: 0h:1m:11s (0h:0m:31s left) +Iteration 120 / LogL: -11222.911 / Time: 0h:1m:18s (0h:0m:24s left) +Iteration 130 / LogL: -11226.630 / Time: 0h:1m:24s (0h:0m:18s left) +Iteration 140 / LogL: -11222.794 / Time: 0h:1m:27s (0h:0m:11s left) +Iteration 150 / LogL: -11223.523 / Time: 0h:1m:33s (0h:0m:5s left) +TREE SEARCH COMPLETED AFTER 159 ITERATIONS / Time: 0h:1m:39s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11224.866 -Optimal log-likelihood: -11224.865 -Rate parameters: A-C: 1.59715 A-G: 2.70642 A-T: 1.82141 C-G: 2.14210 C-T: 2.70642 G-T: 1.00000 +1. Initial log-likelihood: -11222.586 +Optimal log-likelihood: -11222.578 +Rate parameters: A-C: 1.61120 A-G: 2.49430 A-T: 1.81454 C-G: 2.16728 C-T: 2.95194 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 -Proportion of invariable sites: 0.084 -Gamma shape alpha: 1.560 -Parameters optimization took 1 rounds (0.062 sec) -BEST SCORE FOUND : -11224.865 -Total tree length: 12.527 +Proportion of invariable sites: 0.085 +Gamma shape alpha: 1.566 +Parameters optimization took 1 rounds (0.206 sec) +BEST SCORE FOUND : -11222.578 +Total tree length: 12.512 -Total number of iterations: 130 -CPU time used for tree search: 61.978 sec (0h:1m:1s) -Wall-clock time used for tree search: 63.929 sec (0h:1m:3s) -Total CPU time used: 65.909 sec (0h:1m:5s) -Total wall-clock time used: 67.915 sec (0h:1m:7s) +Total number of iterations: 159 +CPU time used for tree search: 58.903 sec (0h:0m:58s) +Wall-clock time used for tree search: 94.235 sec (0h:1m:34s) +Total CPU time used: 62.764 sec (0h:1m:2s) +Total wall-clock time used: 99.299 sec (0h:1m:39s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -4903,19 +4941,21 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Fri Aug 5 07:44:03 2022 -99.07user 0.63system 1:42.56elapsed 97%CPU (0avgtext+0avgdata 14660maxresident)k -0inputs+0outputs (0major+2957minor)pagefaults 0swaps -+ time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo +Date and Time: Sun Jul 4 03:41:17 2021 + +real 2m46.363s +user 1m47.083s +sys 0m1.206s ++ /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos5-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo -Seed: 784485 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Fri Aug 5 07:44:03 2022 -Kernel: AVX - 2 threads (16 CPU cores detected) +Seed: 13070 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Sun Jul 4 03:41:18 2021 +Kernel: AVX - 2 threads (15 CPU cores detected) Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences @@ -4974,271 +5014,278 @@ NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC - 1 JC 11923.628 85 24017.255 24066.316 24353.060 - 2 JC+I 11669.883 86 23511.767 23562.150 23851.522 - 3 JC+G4 11363.296 86 22898.591 22948.975 23238.346 - 4 JC+I+G4 11346.433 87 22866.867 22918.597 23210.573 - 5 JC+R2 11460.283 87 23094.567 23146.297 23438.273 - 6 JC+R3 11349.557 89 22877.115 22931.605 23228.722 - 7 JC+R4 11340.087 91 22862.174 22919.516 23221.682 - 8 JC+R5 11339.948 93 22865.897 22926.187 23233.307 - 14 F81+F 11927.333 88 24030.666 24083.765 24378.323 - 15 F81+F+I 11670.259 89 23518.518 23573.008 23870.125 - 16 F81+F+G4 11358.529 89 22895.058 22949.547 23246.665 - 17 F81+F+I+G4 11341.895 90 22863.789 22919.694 23219.347 - 18 F81+F+R2 11457.886 90 23095.773 23151.677 23451.331 - 19 F81+F+R3 11345.804 92 22875.608 22934.412 23239.067 - 20 F81+F+R4 11335.393 94 22858.786 22920.585 23230.146 - 21 F81+F+R5 11335.282 96 22862.564 22927.455 23241.825 - 27 K2P 11881.076 86 23934.153 23984.537 24273.908 - 28 K2P+I 11627.075 87 23428.149 23479.879 23771.855 - 29 K2P+G4 11316.740 87 22807.480 22859.210 23151.186 - 30 K2P+I+G4 11300.267 88 22776.533 22829.632 23124.190 - 31 K2P+R2 11416.205 88 23008.409 23061.508 23356.066 - 32 K2P+R3 11303.971 90 22787.942 22843.846 23143.500 - 33 K2P+R4 11293.768 92 22771.536 22830.340 23134.995 - 34 K2P+R5 11293.664 94 22775.327 22837.127 23146.688 - 40 HKY+F 11884.045 89 23946.090 24000.580 24297.697 - 41 HKY+F+I 11625.800 90 23431.599 23487.503 23787.157 - 42 HKY+F+G4 11309.303 90 22798.605 22854.510 23154.163 - 43 HKY+F+I+G4 11293.017 91 22768.033 22825.376 23127.542 - 44 HKY+F+R2 11411.536 91 23005.072 23062.415 23364.581 - 45 HKY+F+R3 11297.610 93 22781.221 22841.510 23148.630 - 46 HKY+F+R4 11286.412 95 22762.823 22826.157 23138.134 - 47 HKY+F+R5 11286.351 97 22766.702 22833.178 23149.915 - 53 TNe 11880.065 87 23934.130 23985.859 24277.835 - 54 TNe+I 11620.650 88 23417.300 23470.398 23764.956 - 55 TNe+G4 11315.459 88 22806.918 22860.016 23154.575 - 56 TNe+I+G4 11298.288 89 22774.575 22829.065 23126.182 - 57 TNe+R2 11414.812 89 23007.624 23062.114 23359.232 - 58 TNe+R3 11300.588 91 22783.175 22840.518 23142.684 - 59 TNe+R4 11290.964 93 22767.928 22828.218 23135.338 - 60 TNe+R5 11290.801 95 22771.601 22834.935 23146.913 - 66 TN+F 11882.917 90 23945.834 24001.739 24301.392 - 67 TN+F+I 11618.509 91 23419.019 23476.361 23778.527 - 68 TN+F+G4 11307.383 91 22796.766 22854.108 23156.274 - 69 TN+F+I+G4 11290.263 92 22764.527 22823.331 23127.986 - 70 TN+F+R2 11409.606 92 23003.211 23062.015 23366.670 - 71 TN+F+R3 11293.299 94 22774.598 22836.398 23145.959 - 72 TN+F+R4 11282.625 96 22757.250 22822.142 23136.512 - 73 TN+F+R5 11282.545 98 22761.089 22829.174 23148.252 - 79 K3P 11867.490 87 23908.981 23960.711 24252.687 - 80 K3P+I 11612.745 88 23401.490 23454.588 23749.146 - 81 K3P+G4 11305.537 88 22787.073 22840.172 23134.730 - 82 K3P+I+G4 11288.477 89 22754.954 22809.444 23106.561 - 83 K3P+R2 11401.945 89 22981.891 23036.381 23333.498 - 84 K3P+R3 11291.942 91 22765.885 22823.227 23125.393 - 85 K3P+R4 11282.100 93 22750.200 22810.490 23117.610 - 86 K3P+R5 11282.046 95 22754.092 22817.426 23129.403 - 92 K3Pu+F 11870.569 90 23921.138 23977.043 24276.696 - 93 K3Pu+F+I 11611.617 91 23405.233 23462.576 23764.742 - 94 K3Pu+F+G4 11298.775 91 22779.549 22836.892 23139.058 - 95 K3Pu+F+I+G4 11281.879 92 22747.758 22806.562 23111.217 - 96 K3Pu+F+R2 11397.646 92 22979.292 23038.096 23342.751 - 97 K3Pu+F+R3 11286.226 94 22760.452 22822.251 23131.812 - 98 K3Pu+F+R4 11275.375 96 22742.751 22807.643 23122.013 - 99 K3Pu+F+R5 11275.327 98 22746.654 22814.738 23133.817 -105 TPM2+F 11883.629 90 23947.257 24003.162 24302.815 -106 TPM2+F+I 11625.200 91 23432.400 23489.742 23791.908 -107 TPM2+F+G4 11308.868 91 22799.735 22857.078 23159.244 -108 TPM2+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 -109 TPM2+F+R2 11411.526 92 23007.053 23065.857 23370.512 -110 TPM2+F+R3 11297.355 94 22782.711 22844.510 23154.071 -111 TPM2+F+R4 11286.270 96 22764.539 22829.431 23143.801 -112 TPM2+F+R5 11286.146 98 22768.292 22836.376 23155.455 -118 TPM2u+F 11883.629 90 23947.258 24003.162 24302.815 -119 TPM2u+F+I 11625.201 91 23432.402 23489.745 23791.911 -120 TPM2u+F+G4 11308.867 91 22799.735 22857.077 23159.243 -121 TPM2u+F+I+G4 11292.708 92 22769.416 22828.220 23132.875 -122 TPM2u+F+R2 11411.527 92 23007.053 23065.857 23370.512 -123 TPM2u+F+R3 11297.355 94 22782.710 22844.509 23154.070 -124 TPM2u+F+R4 11286.270 96 22764.540 22829.432 23143.802 -125 TPM2u+F+R5 11286.143 98 22768.285 22836.370 23155.448 -131 TPM3+F 11851.525 90 23883.050 23938.954 24238.608 -132 TPM3+F+I 11613.469 91 23408.938 23466.281 23768.447 -133 TPM3+F+G4 11305.327 91 22792.654 22849.996 23152.162 -134 TPM3+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 -135 TPM3+F+R2 11405.175 92 22994.351 23053.155 23357.810 -136 TPM3+F+R3 11293.007 94 22774.014 22835.813 23145.374 -137 TPM3+F+R4 11283.178 96 22758.356 22823.248 23137.618 -138 TPM3+F+R5 11283.049 98 22762.099 22830.183 23149.262 -144 TPM3u+F 11851.525 90 23883.050 23938.954 24238.608 -145 TPM3u+F+I 11613.469 91 23408.938 23466.281 23768.447 -146 TPM3u+F+G4 11305.327 91 22792.655 22849.997 23152.163 -147 TPM3u+F+I+G4 11289.855 92 22763.711 22822.515 23127.170 -148 TPM3u+F+R2 11405.172 92 22994.345 23053.149 23357.804 -149 TPM3u+F+R3 11293.007 94 22774.014 22835.813 23145.374 -150 TPM3u+F+R4 11283.172 96 22758.344 22823.236 23137.606 -151 TPM3u+F+R5 11283.047 98 22762.095 22830.179 23149.258 -157 TIMe 11866.486 88 23908.972 23962.070 24256.629 -158 TIMe+I 11606.350 89 23390.699 23445.189 23742.306 -159 TIMe+G4 11304.322 89 22786.643 22841.133 23138.250 -160 TIMe+I+G4 11286.570 90 22753.139 22809.044 23108.697 -161 TIMe+R2 11400.580 90 22981.161 23037.065 23336.718 -162 TIMe+R3 11288.530 92 22761.060 22819.864 23124.519 -163 TIMe+R4 11279.399 94 22746.797 22808.596 23118.158 -164 TIMe+R5 11279.309 96 22750.619 22815.511 23129.880 -170 TIM+F 11869.451 91 23920.901 23978.244 24280.410 -171 TIM+F+I 11604.362 92 23392.723 23451.527 23756.182 -172 TIM+F+G4 11296.948 92 22777.895 22836.699 23141.354 -173 TIM+F+I+G4 11279.221 93 22744.442 22804.732 23111.852 -174 TIM+F+R2 11395.723 93 22977.446 23037.735 23344.855 -175 TIM+F+R3 11281.905 95 22753.810 22817.144 23129.121 -176 TIM+F+R4 11271.730 97 22737.460 22803.935 23120.672 -177 TIM+F+R5 11271.695 99 22741.389 22811.107 23132.503 -183 TIM2e 11879.551 88 23935.102 23988.200 24282.758 -184 TIM2e+I 11619.949 89 23417.898 23472.388 23769.506 -185 TIM2e+G4 11315.204 89 22808.409 22862.898 23160.016 -186 TIM2e+I+G4 11298.141 90 22776.282 22832.187 23131.840 -187 TIM2e+R2 11414.742 90 23009.484 23065.388 23365.041 -188 TIM2e+R3 11300.473 92 22784.945 22843.750 23148.405 -189 TIM2e+R4 11290.833 94 22769.667 22831.466 23141.027 -190 TIM2e+R5 11290.739 96 22773.478 22838.370 23152.740 -196 TIM2+F 11882.506 91 23947.012 24004.354 24306.520 -197 TIM2+F+I 11617.928 92 23419.855 23478.659 23783.314 -198 TIM2+F+G4 11306.963 92 22797.925 22856.729 23161.384 -199 TIM2+F+I+G4 11289.986 93 22765.972 22826.262 23133.382 -200 TIM2+F+R2 11409.581 93 23005.161 23065.451 23372.571 -201 TIM2+F+R3 11293.076 95 22776.151 22839.485 23151.462 -202 TIM2+F+R4 11282.473 97 22758.946 22825.422 23142.159 -203 TIM2+F+R5 11282.402 99 22762.805 22832.523 23153.918 -209 TIM3e 11838.747 88 23853.494 23906.592 24201.150 -210 TIM3e+I 11602.540 89 23383.080 23437.570 23734.687 -211 TIM3e+G4 11307.306 89 22792.612 22847.102 23144.219 -212 TIM3e+I+G4 11291.340 90 22762.680 22818.585 23118.238 -213 TIM3e+R2 11403.257 90 22986.514 23042.418 23342.071 -214 TIM3e+R3 11291.597 92 22767.193 22825.997 23130.652 -215 TIM3e+R4 11283.522 94 22755.045 22816.844 23126.405 -216 TIM3e+R5 11283.418 96 22758.835 22823.727 23138.097 -222 TIM3+F 11850.147 91 23882.293 23939.636 24241.802 -223 TIM3+F+I 11606.170 92 23396.339 23455.144 23759.799 -224 TIM3+F+G4 11303.297 92 22790.593 22849.397 23154.052 -225 TIM3+F+I+G4 11287.023 93 22760.046 22820.336 23127.456 -226 TIM3+F+R2 11403.216 93 22992.433 23052.722 23359.842 -227 TIM3+F+R3 11288.650 95 22767.299 22830.632 23142.610 -228 TIM3+F+R4 11279.141 97 22752.282 22818.757 23135.494 -229 TIM3+F+R5 11279.094 99 22756.187 22825.905 23147.301 -235 TVMe 11826.121 89 23830.242 23884.732 24181.849 -236 TVMe+I 11594.361 90 23368.722 23424.627 23724.280 -237 TVMe+G4 11295.606 90 22771.211 22827.116 23126.769 -238 TVMe+I+G4 11280.065 91 22742.130 22799.473 23101.639 -239 TVMe+R2 11390.331 91 22962.661 23020.004 23322.170 -240 TVMe+R3 11281.356 93 22748.713 22809.003 23116.123 -241 TVMe+R4 11273.798 95 22737.595 22800.929 23112.906 -242 TVMe+R5 11273.698 97 22741.396 22807.871 23124.608 -248 TVM+F 11837.769 92 23859.537 23918.341 24222.996 -249 TVM+F+I 11599.049 93 23384.097 23444.387 23751.507 -250 TVM+F+G4 11292.632 93 22771.264 22831.554 23138.674 -251 TVM+F+I+G4 11276.861 94 22741.721 22803.521 23113.082 -252 TVM+F+R2 11390.890 94 22969.780 23031.579 23341.140 -253 TVM+F+R3 11279.704 96 22751.409 22816.301 23130.671 -254 TVM+F+R4 11270.720 98 22737.439 22805.524 23124.602 -255 TVM+F+R5 11270.590 100 22741.181 22812.559 23136.245 -261 SYM 11824.854 90 23829.707 23885.612 24185.265 -262 SYM+I 11587.951 91 23357.902 23415.245 23717.411 -263 SYM+G4 11294.178 91 22770.357 22827.699 23129.865 -264 SYM+I+G4 11278.013 92 22740.027 22798.831 23103.486 -265 SYM+R2 11388.873 92 22961.746 23020.550 23325.205 -266 SYM+R3 11277.825 94 22743.649 22805.449 23115.010 -267 SYM+R4 11270.756 96 22733.511 22798.403 23112.773 -268 SYM+R5 11270.608 98 22737.216 22805.300 23124.379 -274 GTR+F 11836.396 93 23858.792 23919.082 24226.202 -275 GTR+F+I 11591.768 94 23371.536 23433.336 23742.897 -276 GTR+F+G4 11290.699 94 22769.397 22831.197 23140.758 -277 GTR+F+I+G4 11274.183 95 22738.365 22801.698 23113.676 -278 GTR+F+R2 11389.047 95 22968.093 23031.427 23343.404 -279 GTR+F+R3 11275.377 97 22744.753 22811.229 23127.966 -280 GTR+F+R4 11266.912 99 22731.824 22801.543 23122.938 -281 GTR+F+R5 11266.818 101 22735.637 22808.701 23134.652 + 1 JC 12015.193 85 24200.386 24249.447 24536.191 + 2 JC+I 11749.817 86 23671.635 23722.019 24011.390 + 3 JC+G4 11426.892 86 23025.785 23076.169 23365.540 + 4 JC+I+G4 11409.860 87 22993.720 23045.450 23337.426 + 5 JC+R2 11538.548 87 23251.096 23302.826 23594.802 + 6 JC+R3 11416.865 89 23011.730 23066.220 23363.337 + 7 JC+R4 11408.567 91 22999.135 23056.477 23358.643 + 8 JC+R5 11407.459 93 23000.917 23061.207 23368.327 + 14 F81+F 12014.723 88 24205.447 24258.545 24553.103 + 15 F81+F+I 11746.066 89 23670.131 23724.621 24021.738 + 16 F81+F+G4 11418.644 89 23015.289 23069.779 23366.896 + 17 F81+F+I+G4 11401.906 90 22983.812 23039.716 23339.370 + 18 F81+F+R2 11532.431 90 23244.861 23300.766 23600.419 + 19 F81+F+R3 11409.624 92 23003.248 23062.052 23366.707 + 20 F81+F+R4 11399.419 94 22986.839 23048.638 23358.199 + 21 F81+F+R5 11399.287 96 22990.575 23055.467 23369.836 + 27 K2P 11970.818 86 24113.636 24164.020 24453.391 + 28 K2P+I 11705.384 87 23584.767 23636.497 23928.473 + 29 K2P+G4 11377.365 87 22928.730 22980.460 23272.436 + 30 K2P+I+G4 11360.860 88 22897.720 22950.818 23245.377 + 31 K2P+R2 11491.642 88 23159.283 23212.382 23506.940 + 32 K2P+R3 11368.396 90 22916.792 22972.696 23272.350 + 33 K2P+R4 11358.063 92 22900.125 22958.930 23263.584 + 34 K2P+R5 11358.037 94 22904.074 22965.874 23275.435 + 40 HKY+F 11969.910 89 24117.819 24172.309 24469.426 + 41 HKY+F+I 11700.293 90 23580.586 23636.490 23936.144 + 42 HKY+F+G4 11366.737 90 22913.475 22969.379 23269.032 + 43 HKY+F+I+G4 11350.329 91 22882.659 22940.001 23242.167 + 44 HKY+F+R2 11483.520 91 23149.039 23206.382 23508.548 + 45 HKY+F+R3 11358.705 93 22903.410 22963.700 23270.820 + 46 HKY+F+R4 11347.352 95 22884.703 22948.037 23260.014 + 47 HKY+F+R5 11347.339 97 22888.678 22955.154 23271.891 + 53 TNe 11969.088 87 24112.176 24163.906 24455.882 + 54 TNe+I 11696.852 88 23569.705 23622.803 23917.361 + 55 TNe+G4 11374.378 88 22924.756 22977.854 23272.412 + 56 TNe+I+G4 11357.169 89 22892.337 22946.827 23243.945 + 57 TNe+R2 11489.369 89 23156.738 23211.228 23508.345 + 58 TNe+R3 11362.661 91 22907.323 22964.665 23266.831 + 59 TNe+R4 11353.344 93 22892.689 22952.978 23260.098 + 60 TNe+R5 11353.332 95 22896.664 22959.997 23271.975 + 66 TN+F 11968.110 90 24116.221 24172.125 24471.779 + 67 TN+F+I 11690.996 91 23563.992 23621.335 23923.501 + 68 TN+F+G4 11362.959 91 22907.919 22965.261 23267.427 + 69 TN+F+I+G4 11345.763 92 22875.526 22934.330 23238.985 + 70 TN+F+R2 11480.714 92 23145.429 23204.233 23508.888 + 71 TN+F+R3 11351.854 94 22891.708 22953.507 23263.068 + 72 TN+F+R4 11341.711 96 22875.421 22940.313 23254.683 + 73 TN+F+R5 11341.613 98 22879.227 22947.311 23266.390 + 79 K3P 11955.726 87 24085.452 24137.182 24429.158 + 80 K3P+I 11689.786 88 23555.572 23608.670 23903.229 + 81 K3P+G4 11366.551 88 22909.101 22962.200 23256.758 + 82 K3P+I+G4 11349.411 89 22876.821 22931.311 23228.429 + 83 K3P+R2 11477.146 89 23132.292 23186.782 23483.899 + 84 K3P+R3 11357.300 91 22896.599 22953.942 23256.108 + 85 K3P+R4 11346.132 93 22878.264 22938.554 23245.674 + 86 K3P+R5 11346.075 95 22882.150 22945.483 23257.461 + 92 K3Pu+F 11954.797 90 24089.594 24145.498 24445.152 + 93 K3Pu+F+I 11684.711 91 23551.421 23608.764 23910.930 + 94 K3Pu+F+G4 11356.428 91 22894.856 22952.198 23254.364 + 95 K3Pu+F+I+G4 11339.416 92 22862.833 22921.637 23226.292 + 96 K3Pu+F+R2 11469.398 92 23122.796 23181.600 23486.255 + 97 K3Pu+F+R3 11348.095 94 22884.191 22945.990 23255.551 + 98 K3Pu+F+R4 11335.892 96 22863.784 22928.676 23243.046 + 99 K3Pu+F+R5 11335.816 98 22867.632 22935.716 23254.795 +105 TPM2+F 11969.902 90 24119.804 24175.708 24475.361 +106 TPM2+F+I 11700.222 91 23582.444 23639.787 23941.953 +107 TPM2+F+G4 11365.880 91 22913.760 22971.103 23273.269 +108 TPM2+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 +109 TPM2+F+R2 11483.376 92 23150.752 23209.556 23514.211 +110 TPM2+F+R3 11358.087 94 22904.173 22965.972 23275.533 +111 TPM2+F+R4 11346.136 96 22884.272 22949.164 23263.533 +112 TPM2+F+R5 11346.063 98 22888.126 22956.210 23275.289 +118 TPM2u+F 11969.903 90 24119.805 24175.710 24475.363 +119 TPM2u+F+I 11700.223 91 23582.445 23639.788 23941.954 +120 TPM2u+F+G4 11365.880 91 22913.760 22971.102 23273.268 +121 TPM2u+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 +122 TPM2u+F+R2 11483.380 92 23150.760 23209.564 23514.219 +123 TPM2u+F+R3 11358.086 94 22904.173 22965.972 23275.533 +124 TPM2u+F+R4 11346.012 96 22884.023 22948.915 23263.285 +125 TPM2u+F+R5 11346.004 98 22888.009 22956.093 23275.172 +131 TPM3+F 11939.208 90 24058.415 24114.320 24413.973 +132 TPM3+F+I 11688.861 91 23559.723 23617.065 23919.231 +133 TPM3+F+G4 11362.780 91 22907.560 22964.903 23267.069 +134 TPM3+F+I+G4 11347.020 92 22878.039 22936.843 23241.498 +135 TPM3+F+R2 11476.513 92 23137.026 23195.830 23500.485 +136 TPM3+F+R3 11353.918 94 22895.835 22957.634 23267.196 +137 TPM3+F+R4 11342.967 96 22877.935 22942.827 23257.196 +138 TPM3+F+R5 11342.922 98 22881.844 22949.928 23269.007 +144 TPM3u+F 11939.209 90 24058.418 24114.323 24413.976 +145 TPM3u+F+I 11688.862 91 23559.723 23617.066 23919.232 +146 TPM3u+F+G4 11362.781 91 22907.561 22964.904 23267.070 +147 TPM3u+F+I+G4 11347.020 92 22878.040 22936.844 23241.499 +148 TPM3u+F+R2 11476.515 92 23137.030 23195.834 23500.489 +149 TPM3u+F+R3 11353.918 94 22895.835 22957.634 23267.195 +150 TPM3u+F+R4 11342.887 96 22877.774 22942.666 23257.036 +151 TPM3u+F+R5 11342.887 98 22881.774 22949.858 23268.937 +157 TIMe 11954.065 88 24084.129 24137.228 24431.786 +158 TIMe+I 11681.462 89 23540.924 23595.413 23892.531 +159 TIMe+G4 11363.653 89 22905.306 22959.796 23256.913 +160 TIMe+I+G4 11345.802 90 22871.603 22927.508 23227.161 +161 TIMe+R2 11475.095 90 23130.189 23186.094 23485.747 +162 TIMe+R3 11351.551 92 22887.101 22945.905 23250.560 +163 TIMe+R4 11341.268 94 22870.536 22932.335 23241.896 +164 TIMe+R5 11341.264 96 22874.528 22939.420 23253.790 +170 TIM+F 11953.073 91 24088.145 24145.488 24447.654 +171 TIM+F+I 11675.638 92 23535.276 23594.080 23898.735 +172 TIM+F+G4 11352.739 92 22889.478 22948.282 23252.937 +173 TIM+F+I+G4 11334.933 93 22855.867 22916.156 23223.276 +174 TIM+F+R2 11466.803 93 23119.606 23179.896 23487.016 +175 TIM+F+R3 11341.217 95 22872.434 22935.768 23247.745 +176 TIM+F+R4 11330.083 97 22854.165 22920.641 23237.378 +177 TIM+F+R5 11330.040 99 22858.080 22927.799 23249.194 +183 TIM2e 11969.060 88 24114.119 24167.218 24461.776 +184 TIM2e+I 11696.724 89 23571.449 23625.939 23923.056 +185 TIM2e+G4 11373.751 89 22925.503 22979.993 23277.110 +186 TIM2e+I+G4 11356.625 90 22893.250 22949.154 23248.808 +187 TIM2e+R2 11489.326 90 23158.651 23214.556 23514.209 +188 TIM2e+R3 11362.313 92 22908.626 22967.431 23272.086 +189 TIM2e+R4 11352.064 94 22892.128 22953.927 23263.488 +190 TIM2e+R5 11352.061 96 22896.122 22961.014 23275.384 +196 TIM2+F 11968.103 91 24118.206 24175.549 24477.715 +197 TIM2+F+I 11690.924 92 23565.848 23624.653 23929.308 +198 TIM2+F+G4 11362.111 92 22908.222 22967.027 23271.682 +199 TIM2+F+I+G4 11345.003 93 22876.007 22936.297 23243.417 +200 TIM2+F+R2 11480.623 93 23147.246 23207.536 23514.656 +201 TIM2+F+R3 11351.348 95 22892.696 22956.029 23268.007 +202 TIM2+F+R4 11340.298 97 22874.597 22941.072 23257.809 +203 TIM2+F+R5 11340.262 99 22878.523 22948.242 23269.637 +209 TIM3e 11929.583 88 24035.165 24088.263 24382.822 +210 TIM3e+I 11679.665 89 23537.329 23591.819 23888.937 +211 TIM3e+G4 11366.249 89 22910.499 22964.989 23262.106 +212 TIM3e+I+G4 11350.100 90 22880.199 22936.103 23235.757 +213 TIM3e+R2 11477.347 90 23134.694 23190.598 23490.252 +214 TIM3e+R3 11353.723 92 22891.445 22950.249 23254.904 +215 TIM3e+R4 11345.129 94 22878.259 22940.058 23249.619 +216 TIM3e+R5 11345.116 96 22882.233 22947.125 23261.494 +222 TIM3+F 11937.046 91 24056.091 24113.433 24415.599 +223 TIM3+F+I 11679.411 92 23542.822 23601.627 23906.282 +224 TIM3+F+G4 11358.813 92 22901.625 22960.429 23265.084 +225 TIM3+F+I+G4 11342.334 93 22870.668 22930.957 23238.077 +226 TIM3+F+R2 11473.687 93 23133.374 23193.664 23500.784 +227 TIM3+F+R3 11347.077 95 22884.154 22947.488 23259.465 +228 TIM3+F+R4 11337.180 97 22868.361 22934.836 23251.573 +229 TIM3+F+R5 11337.160 99 22872.319 22942.037 23263.433 +235 TVMe 11915.914 89 24009.828 24064.317 24361.435 +236 TVMe+I 11672.235 90 23524.469 23580.374 23880.027 +237 TVMe+G4 11355.962 90 22891.924 22947.828 23247.481 +238 TVMe+I+G4 11340.052 91 22862.103 22919.446 23221.612 +239 TVMe+R2 11464.332 91 23110.664 23168.006 23470.172 +240 TVMe+R3 11345.869 93 22877.738 22938.028 23245.148 +241 TVMe+R4 11336.465 95 22862.930 22926.264 23238.242 +242 TVMe+R5 11336.449 97 22866.898 22933.374 23250.111 +248 TVM+F 11923.307 92 24030.614 24089.418 24394.073 +249 TVM+F+I 11672.689 93 23531.379 23591.668 23898.789 +250 TVM+F+G4 11349.481 93 22884.961 22945.251 23252.371 +251 TVM+F+I+G4 11333.273 94 22854.547 22916.346 23225.907 +252 TVM+F+R2 11461.206 94 23110.412 23172.211 23481.772 +253 TVM+F+R3 11340.584 96 22873.169 22938.061 23252.431 +254 TVM+F+R4 11329.650 98 22855.299 22923.383 23242.462 +255 TVM+F+R5 11329.621 100 22859.241 22930.619 23254.305 +261 SYM 11913.886 90 24007.771 24063.676 24363.329 +262 SYM+I 11663.801 91 23509.602 23566.945 23869.111 +263 SYM+G4 11352.816 91 22887.633 22944.975 23247.141 +264 SYM+I+G4 11336.290 92 22856.581 22915.385 23220.040 +265 SYM+R2 11462.111 92 23108.223 23167.027 23471.682 +266 SYM+R3 11340.196 94 22868.392 22930.192 23239.753 +267 SYM+R4 11332.021 96 22856.043 22920.935 23235.305 +268 SYM+R5 11332.007 98 22860.014 22928.098 23247.177 +274 GTR+F 11921.235 93 24028.470 24088.759 24395.880 +275 GTR+F+I 11663.491 94 23514.982 23576.782 23886.343 +276 GTR+F+G4 11345.623 94 22879.246 22941.045 23250.606 +277 GTR+F+I+G4 11328.789 95 22847.578 22910.912 23222.890 +278 GTR+F+R2 11458.594 95 23107.189 23170.522 23482.500 +279 GTR+F+R3 11333.883 97 22861.767 22928.242 23244.979 +280 GTR+F+R4 11324.370 99 22846.739 22916.457 23237.853 +281 GTR+F+R5 11324.349 101 22850.699 22923.762 23249.713 Akaike Information Criterion: GTR+F+R4 -Corrected Akaike Information Criterion: SYM+R4 -Bayesian Information Criterion: TVMe+I+G4 -Best-fit model: TVMe+I+G4 chosen according to BIC +Corrected Akaike Information Criterion: GTR+F+I+G4 +Bayesian Information Criterion: SYM+I+G4 +Best-fit model: SYM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 0.076 seconds (0h:0m:0s) -Wall-clock time for ModelFinder: 0.077 seconds (0h:0m:0s) +CPU time for ModelFinder: 0.087 seconds (0h:0m:0s) +Wall-clock time for ModelFinder: 0.192 seconds (0h:0m:0s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... -Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.956 / LogL: -11295.603 -Init pinv, alpha: 0.012, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.077 -Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.570 / LogL: -11280.070 -Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.568 / LogL: -11280.070 -Init pinv, alpha: 0.046, 1.000 / Estimate: 0.085, 1.571 / LogL: -11280.067 -Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.569 / LogL: -11280.068 -Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.573 / LogL: -11280.065 -Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.575 / LogL: -11280.064 -Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.064 -Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.579 / LogL: -11280.065 -Optimal pinv,alpha: 0.085, 1.575 / LogL: -11280.064 +Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.872 / LogL: -11352.830 +Init pinv, alpha: 0.012, 1.000 / Estimate: 0.086, 1.479 / LogL: -11336.284 +Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.484 / LogL: -11336.280 +Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 +Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.486 / LogL: -11336.278 +Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 +Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.485 / LogL: -11336.279 +Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.487 / LogL: -11336.278 +Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.488 / LogL: -11336.278 +Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.490 / LogL: -11336.278 +Optimal pinv,alpha: 0.087, 1.488 / LogL: -11336.278 -Parameters optimization took 2.418 sec -Computing ML distances based on estimated model parameters... 0.025 sec +Parameters optimization took 12.412 sec +Computing ML distances based on estimated model parameters... 0.040 sec Computing BIONJ tree... 0.002 seconds -Log-likelihood of BIONJ tree: -11256.375 +Log-likelihood of BIONJ tree: -11256.524 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 0.949 second -Computing log-likelihood of 98 initial trees ... 2.779 seconds -Current best score: -11230.916 +Generating 98 parsimony trees... 2.427 second +Computing log-likelihood of 98 initial trees ... 6.947 seconds +Current best score: -11234.904 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11225.741 +BETTER TREE FOUND at iteration 1: -11229.869 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 2: -11224.594 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 9: -11225.461 -Iteration 10 / LogL: -11227.958 / Time: 0h:0m:8s +BETTER TREE FOUND at iteration 4: -11224.232 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 15: -11224.864 -Iteration 20 / LogL: -11231.326 / Time: 0h:0m:10s -Finish initializing candidate tree set (14) -Current best tree score: -11224.864 / CPU time: 8.071 +BETTER TREE FOUND at iteration 6: -11223.763 +Iteration 10 / LogL: -11229.722 / Time: 0h:0m:27s +Iteration 20 / LogL: -11229.422 / Time: 0h:0m:31s +Finish initializing candidate tree set (12) +Current best tree score: -11223.763 / CPU time: 18.918 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -11225.318 / Time: 0h:0m:14s (0h:0m:41s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 40: -11222.801 -Iteration 40 / LogL: -11222.801 / Time: 0h:0m:17s (0h:0m:44s left) +BETTER TREE FOUND at iteration 25: -11222.142 +Iteration 30 / LogL: -11222.205 / Time: 0h:0m:40s (0h:2m:14s left) +Iteration 40 / LogL: -11222.184 / Time: 0h:0m:52s (0h:1m:54s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 48: -11222.783 -Iteration 50 / LogL: -11223.657 / Time: 0h:0m:20s (0h:0m:40s left) -Iteration 60 / LogL: -11223.455 / Time: 0h:0m:22s (0h:0m:34s left) -Iteration 70 / LogL: -11222.830 / Time: 0h:0m:25s (0h:0m:28s left) -Iteration 80 / LogL: -11222.805 / Time: 0h:0m:28s (0h:0m:24s left) -Iteration 90 / LogL: -11222.784 / Time: 0h:0m:30s (0h:0m:20s left) -Iteration 100 / LogL: -11223.065 / Time: 0h:0m:33s (0h:0m:16s left) -Iteration 110 / LogL: -11231.740 / Time: 0h:0m:36s (0h:0m:12s left) -Iteration 120 / LogL: -11225.027 / Time: 0h:0m:38s (0h:0m:9s left) -Iteration 130 / LogL: -11223.056 / Time: 0h:0m:41s (0h:0m:5s left) -Iteration 140 / LogL: -11222.937 / Time: 0h:0m:44s (0h:0m:2s left) -TREE SEARCH COMPLETED AFTER 149 ITERATIONS / Time: 0h:0m:47s +BETTER TREE FOUND at iteration 42: -11221.575 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 46: -11221.030 +Iteration 50 / LogL: -11228.112 / Time: 0h:0m:59s (0h:1m:56s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 57: -11220.891 +Iteration 60 / LogL: -11220.923 / Time: 0h:1m:1s (0h:1m:41s left) +Iteration 70 / LogL: -11220.898 / Time: 0h:1m:4s (0h:1m:21s left) +Iteration 80 / LogL: -11221.060 / Time: 0h:1m:12s (0h:1m:10s left) +Iteration 90 / LogL: -11221.868 / Time: 0h:1m:29s (0h:1m:7s left) +Iteration 100 / LogL: -11221.110 / Time: 0h:1m:42s (0h:0m:59s left) +Iteration 110 / LogL: -11221.725 / Time: 0h:1m:55s (0h:0m:49s left) +Iteration 120 / LogL: -11220.893 / Time: 0h:2m:18s (0h:0m:43s left) +Iteration 130 / LogL: -11221.227 / Time: 0h:2m:44s (0h:0m:34s left) +Iteration 140 / LogL: -11221.052 / Time: 0h:2m:50s (0h:0m:20s left) +Iteration 150 / LogL: -11225.796 / Time: 0h:3m:12s (0h:0m:9s left) +TREE SEARCH COMPLETED AFTER 158 ITERATIONS / Time: 0h:3m:33s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11222.783 -Optimal log-likelihood: -11222.780 -Rate parameters: A-C: 1.50033 A-G: 2.57814 A-T: 1.65222 C-G: 1.95798 C-T: 2.57814 G-T: 1.00000 +1. Initial log-likelihood: -11220.891 +Optimal log-likelihood: -11220.890 +Rate parameters: A-C: 1.52469 A-G: 2.42492 A-T: 1.66566 C-G: 1.99473 C-T: 2.82957 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 -Gamma shape alpha: 1.529 -Parameters optimization took 1 rounds (0.044 sec) -BEST SCORE FOUND : -11222.780 -Total tree length: 12.601 +Gamma shape alpha: 1.533 +Parameters optimization took 1 rounds (0.255 sec) +BEST SCORE FOUND : -11220.890 +Total tree length: 12.593 -Total number of iterations: 149 -CPU time used for tree search: 86.715 sec (0h:1m:26s) -Wall-clock time used for tree search: 44.720 sec (0h:0m:44s) -Total CPU time used: 91.765 sec (0h:1m:31s) -Total wall-clock time used: 47.297 sec (0h:0m:47s) +Total number of iterations: 158 +CPU time used for tree search: 192.886 sec (0h:3m:12s) +Wall-clock time used for tree search: 200.912 sec (0h:3m:20s) +Total CPU time used: 204.959 sec (0h:3m:24s) +Total wall-clock time used: 213.846 sec (0h:3m:33s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -5246,12 +5293,14 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Fri Aug 5 07:44:51 2022 -91.87user 0.88system 0:47.41elapsed 195%CPU (0avgtext+0avgdata 13940maxresident)k -0inputs+0outputs (0major+1291minor)pagefaults 0swaps -+ rm -rf /tmp/iqtree-test.aErHl0 -190.97user 1.53system 2:30.05elapsed 128%CPU (0avgtext+0avgdata 14660maxresident)k -0inputs+0outputs (0major+5834minor)pagefaults 0swaps +Date and Time: Sun Jul 4 03:44:52 2021 + +real 3m34.130s +user 3m25.085s +sys 0m1.825s ++ rm -rf /tmp/iqtree-test.G6Cjoh +312.21user 3.04system 6:20.81elapsed 82%CPU (0avgtext+0avgdata 14944maxresident)k +752inputs+0outputs (21major+6708minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' create-stamp debian/debhelper-build-stamp @@ -5262,7 +5311,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_install -Bbuild.omp - cd build.omp && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.omp && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks @@ -5274,8 +5323,6 @@ make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend @@ -5283,68 +5330,70 @@ make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/nclextra /build/iqtree-1.6.9+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/whtest /build/iqtree-1.6.9+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/nclextra /build/iqtree-1.6.9+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/whtest /build/iqtree-1.6.9+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/sprng /build/iqtree-1.6.9+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/vectorclass /build/iqtree-1.6.9+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 3%] Built target vectorclass -[ 3%] Built target lbfgsb +[ 2%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +[ 3%] Built target vectorclass +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 7%] Built target gsl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 7%] Built target gsl -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 8%] Built target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +[ 12%] Built target sprng +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -[ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' @@ -5354,27 +5403,25 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 15%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 25%] Built target ncl +[ 22%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pda /build/iqtree-1.6.9+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +[ 25%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pda /build/iqtree-1.6.9+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 41%] Built target pll make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 42%] Built target kernelavx make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' @@ -5387,24 +5434,26 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' +[ 26%] Built target kernelavx +[ 42%] Built target pll [ 43%] Built target kernelfma +[ 44%] Built target kernelsse +[ 49%] Built target utils +[ 55%] Built target whtest +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build -[ 44%] Built target kernelsse +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' +cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' -[ 50%] Built target whtest -[ 55%] Built target utils -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 64%] Built target pda -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' -cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= [ 68%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build @@ -5449,7 +5498,7 @@ -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' dh_auto_install -Bbuild.serial - cd build.serial && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.serial && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks @@ -5458,56 +5507,61 @@ make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +[ 2%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 3%] Built target vectorclass +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' @@ -5516,28 +5570,23 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 3%] Built target lbfgsb -[ 3%] Built target vectorclass -[ 7%] Built target gsl -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -[ 8%] Built target pllavx -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 12%] Built target sprng +[ 7%] Built target gsl +[ 8%] Built target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +[ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' @@ -5545,52 +5594,52 @@ make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 15%] Built target nclextra -[ 25%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 25%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 41%] Built target pll make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 42%] Built target kernelsse -[ 43%] Built target kernelavx make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' -make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. +make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +[ 42%] Built target kernelavx +[ 43%] Built target kernelfma +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 44%] Built target kernelsse +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -[ 44%] Built target kernelfma make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' -[ 50%] Built target whtest -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' +[ 50%] Built target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 55%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend -[ 64%] Built target pda -[ 68%] Built target alignment +[ 59%] Built target alignment +[ 68%] Built target pda make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/model /build/iqtree-1.6.9+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' @@ -5634,7 +5683,7 @@ -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' dh_auto_install -Bbuild.mpi - cd build.mpi && make -j16 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.mpi && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks @@ -5662,37 +5711,37 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/gsl /build/iqtree-1.6.9+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/ncl /build/iqtree-1.6.9+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build [ 1%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend [ 2%] Built target vectorclass @@ -5701,16 +5750,16 @@ make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -[ 6%] Built target gsl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +[ 6%] Built target gsl [ 10%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build @@ -5720,26 +5769,26 @@ make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build -make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -[ 11%] Built target pllavx -[ 14%] Built target nclextra -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 13%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +[ 14%] Built target pllavx [ 24%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/alignment /build/iqtree-1.6.9+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' @@ -5753,12 +5802,12 @@ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 25%] Built target kernelavx [ 26%] Built target kernelfma -make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 27%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/mympi.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 28%] Built target mympi make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. @@ -5770,23 +5819,23 @@ make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build -[ 49%] Built target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' +[ 49%] Built target whtest [ 54%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 63%] Built target pda +[ 67%] Built target alignment make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/model /build/iqtree-1.6.9+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= -[ 67%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' @@ -5872,20 +5921,22 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'iqtree' in '../iqtree_1.6.9+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_1.6.9+dfsg-1_amd64.deb'. +dpkg-deb: building package 'iqtree' in '../iqtree_1.6.9+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iqtree_1.6.9+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/42517/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/42517/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/39253 and its subdirectories -I: Current time: Fri Aug 5 07:46:02 -12 2022 -I: pbuilder-time-stamp: 1659728762 +I: removing directory /srv/workspace/pbuilder/42517 and its subdirectories +I: Current time: Sun Jul 4 03:47:02 +14 2021 +I: pbuilder-time-stamp: 1625320022