Diff of the two buildlogs: -- --- b1/build.log 2021-12-28 13:02:00.501255096 +0000 +++ b2/build.log 2021-12-28 13:16:16.066563890 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jan 30 07:08:51 -12 2023 -I: pbuilder-time-stamp: 1675105731 +I: Current time: Wed Dec 29 03:02:02 +14 2021 +I: pbuilder-time-stamp: 1640696522 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./iqtree_1.6.12+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.sZsNX4PM/trustedkeys.kbx': General error -gpgv: Signature made Wed Dec 4 01:13:46 2019 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.3TtO585k/trustedkeys.kbx': General error +gpgv: Signature made Thu Dec 5 03:13:46 2019 +14 gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key @@ -27,135 +27,169 @@ dpkg-source: info: unpacking iqtree_1.6.12+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/270558/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1732826/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/1732826/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1732826/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,-fixfilepath 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]="1" [2]="4" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath 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='d53e6a728d024b5d820149d3e7b8258d' - 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='270558' - PS1='# ' - PS2='> ' + INVOCATION_ID=58bc4e2e1dcb4687a91b4ccede121d38 + 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=1732826 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.vc1JSf81EI/pbuilderrc_pHFU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.vc1JSf81EI/b1 --logfile b1/build.log iqtree_1.6.12+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://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.vc1JSf81EI/pbuilderrc_3cGv --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.vc1JSf81EI/b2 --logfile b2/build.log iqtree_1.6.12+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 ionos15-amd64 5.14.0-0.bpo.2-amd64 #1 SMP Debian 5.14.9-2~bpo11+1 (2021-10-10) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-10-amd64 #1 SMP Debian 5.10.84-1 (2021-12-08) x86_64 GNU/Linux I: ls -l /bin total 5476 - -rwxr-xr-x 1 root root 1234376 Aug 4 2021 bash - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 18424 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 43936 Sep 23 2020 cat - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chgrp - -rwxr-xr-x 1 root root 64448 Sep 23 2020 chmod - -rwxr-xr-x 1 root root 72672 Sep 23 2020 chown - -rwxr-xr-x 1 root root 151168 Sep 23 2020 cp - -rwxr-xr-x 1 root root 125560 Dec 10 2020 dash - -rwxr-xr-x 1 root root 113664 Sep 23 2020 date - -rwxr-xr-x 1 root root 80968 Sep 23 2020 dd - -rwxr-xr-x 1 root root 93936 Sep 23 2020 df - -rwxr-xr-x 1 root root 147176 Sep 23 2020 dir - -rwxr-xr-x 1 root root 84440 Jul 28 2021 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 39712 Sep 23 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 39680 Sep 23 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 69032 Jul 28 2021 findmnt - -rwsr-xr-x 1 root root 34896 Feb 26 2021 fusermount - -rwxr-xr-x 1 root root 203072 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 2021 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 2021 gzexe - -rwxr-xr-x 1 root root 98048 Mar 2 2021 gzip - -rwxr-xr-x 1 root root 22600 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 72840 Sep 23 2020 ln - -rwxr-xr-x 1 root root 56952 Feb 7 2020 login - -rwxr-xr-x 1 root root 147176 Sep 23 2020 ls - -rwxr-xr-x 1 root root 149736 Jul 28 2021 lsblk - -rwxr-xr-x 1 root root 85184 Sep 23 2020 mkdir - -rwxr-xr-x 1 root root 76896 Sep 23 2020 mknod - -rwxr-xr-x 1 root root 48064 Sep 23 2020 mktemp - -rwxr-xr-x 1 root root 59632 Jul 28 2021 more - -rwsr-xr-x 1 root root 55528 Jul 28 2021 mount - -rwxr-xr-x 1 root root 18664 Jul 28 2021 mountpoint - -rwxr-xr-x 1 root root 147080 Sep 23 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 2021 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43872 Sep 23 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 2021 rbash -> bash - -rwxr-xr-x 1 root root 52032 Sep 23 2020 readlink - -rwxr-xr-x 1 root root 72704 Sep 23 2020 rm - -rwxr-xr-x 1 root root 52032 Sep 23 2020 rmdir - -rwxr-xr-x 1 root root 27472 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jan 23 03:47 sh -> dash - -rwxr-xr-x 1 root root 43808 Sep 23 2020 sleep - -rwxr-xr-x 1 root root 84928 Sep 23 2020 stty - -rwsr-xr-x 1 root root 71912 Jul 28 2021 su - -rwxr-xr-x 1 root root 39744 Sep 23 2020 sync - -rwxr-xr-x 1 root root 531928 Feb 16 2021 tar - -rwxr-xr-x 1 root root 14456 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 101408 Sep 23 2020 touch - -rwxr-xr-x 1 root root 39680 Sep 23 2020 true - -rwxr-xr-x 1 root root 14328 Feb 26 2021 ulockmgr_server - -rwsr-xr-x 1 root root 35040 Jul 28 2021 umount - -rwxr-xr-x 1 root root 39744 Sep 23 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 2021 uncompress - -rwxr-xr-x 1 root root 147176 Sep 23 2020 vdir - -rwxr-xr-x 1 root root 63744 Jul 28 2021 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 2021 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 2021 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 2021 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 2021 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 2021 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 2021 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 2021 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 2021 zless - -rwxr-xr-x 1 root root 1842 Mar 2 2021 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 2021 znew -I: user script /srv/workspace/pbuilder/270558/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1234376 Aug 5 10:25 bash + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 18424 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 43936 Sep 24 2020 cat + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chgrp + -rwxr-xr-x 1 root root 64448 Sep 24 2020 chmod + -rwxr-xr-x 1 root root 72672 Sep 24 2020 chown + -rwxr-xr-x 1 root root 151168 Sep 24 2020 cp + -rwxr-xr-x 1 root root 125560 Dec 11 2020 dash + -rwxr-xr-x 1 root root 113664 Sep 24 2020 date + -rwxr-xr-x 1 root root 80968 Sep 24 2020 dd + -rwxr-xr-x 1 root root 93936 Sep 24 2020 df + -rwxr-xr-x 1 root root 147176 Sep 24 2020 dir + -rwxr-xr-x 1 root root 84440 Jul 29 09:09 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 39712 Sep 24 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 39680 Sep 24 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 69032 Jul 29 09:09 findmnt + -rwsr-xr-x 1 root root 34896 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 203072 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 98048 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 22600 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 72840 Sep 24 2020 ln + -rwxr-xr-x 1 root root 56952 Feb 8 2020 login + -rwxr-xr-x 1 root root 147176 Sep 24 2020 ls + -rwxr-xr-x 1 root root 149736 Jul 29 09:09 lsblk + -rwxr-xr-x 1 root root 85184 Sep 24 2020 mkdir + -rwxr-xr-x 1 root root 76896 Sep 24 2020 mknod + -rwxr-xr-x 1 root root 48064 Sep 24 2020 mktemp + -rwxr-xr-x 1 root root 59632 Jul 29 09:09 more + -rwsr-xr-x 1 root root 55528 Jul 29 09:09 mount + -rwxr-xr-x 1 root root 18664 Jul 29 09:09 mountpoint + -rwxr-xr-x 1 root root 147080 Sep 24 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43872 Sep 24 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash + -rwxr-xr-x 1 root root 52032 Sep 24 2020 readlink + -rwxr-xr-x 1 root root 72704 Sep 24 2020 rm + -rwxr-xr-x 1 root root 52032 Sep 24 2020 rmdir + -rwxr-xr-x 1 root root 27472 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Dec 29 03:02 sh -> bash + lrwxrwxrwx 1 root root 4 Dec 21 23:24 sh.distrib -> dash + -rwxr-xr-x 1 root root 43808 Sep 24 2020 sleep + -rwxr-xr-x 1 root root 84928 Sep 24 2020 stty + -rwsr-xr-x 1 root root 71912 Jul 29 09:09 su + -rwxr-xr-x 1 root root 39744 Sep 24 2020 sync + -rwxr-xr-x 1 root root 531928 Feb 17 2021 tar + -rwxr-xr-x 1 root root 14456 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 101408 Sep 24 2020 touch + -rwxr-xr-x 1 root root 39680 Sep 24 2020 true + -rwxr-xr-x 1 root root 14328 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 35040 Jul 29 09:09 umount + -rwxr-xr-x 1 root root 39744 Sep 24 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 147176 Sep 24 2020 vdir + -rwxr-xr-x 1 root root 63744 Jul 29 09:09 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/1732826/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -321,7 +355,7 @@ Get: 112 http://deb.debian.org/debian bullseye/main amd64 libsprng2-dev amd64 2.0a-13 [77.9 kB] Get: 113 http://deb.debian.org/debian bullseye/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get: 114 http://deb.debian.org/debian bullseye/main amd64 time amd64 1.9-0.1 [50.8 kB] -Fetched 56.5 MB in 1s (50.3 MB/s) +Fetched 56.5 MB in 2s (37.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19655 files and directories currently installed.) @@ -803,7 +837,8 @@ fakeroot is already the newest version (1.25.3-1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/iqtree-1.6.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iqtree_1.6.12+dfsg-1_source.changes +hostname: Name or service not known +I: Running cd /build/iqtree-1.6.12+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iqtree_1.6.12+dfsg-1_source.changes dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 1.6.12+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -990,7 +1025,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-1.6.12+dfsg' dh_auto_build -Bbuild.omp - cd build.omp && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 + cd build.omp && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.12+dfsg/build.omp//CMakeFiles/progress.marks @@ -998,157 +1033,180 @@ make[3]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' 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 -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/gsl /build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/ncl /build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/depend.internal". -Scanning dependencies of target gsl -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/depend.internal". +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.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-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/nclextra /build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/whtest /build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/sprng /build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/vectorclass /build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Dependee "/build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/depend.internal". Scanning dependencies of target lbfgsb -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/depend.internal". -Scanning dependencies of target ncl +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/depend.internal". -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/depend.internal". +Scanning dependencies of target gsl Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/depend.internal". -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/depend.internal". +Scanning dependencies of target vectorclass +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/depend.internal". +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +Scanning dependencies of target pllavx make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/nclextra /build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/depend.internal". make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/whtest /build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -Scanning dependencies of target pllavx make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/sprng /build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -Scanning dependencies of target pll -Scanning dependencies of target kernelfma +Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/binomial_tpe.cpp -[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +Scanning dependencies of target nclextra +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -Scanning dependencies of target kernelavx -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -[ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +Scanning dependencies of target whtest +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 0%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +[ 3%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +[ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +Scanning dependencies of target ncl cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/multinomial.cpp +cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/pow_int.cpp +cd /build/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/vectorclass/instrset_detect.cpp Scanning dependencies of target kernelsse +cd /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +Scanning dependencies of target kernelfma +cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/binomial_tpe.cpp +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp +Scanning dependencies of target kernelavx +[ 4%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -[ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +Scanning dependencies of target pll make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/avxLikelihood.c +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/pow_int.cpp -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/depend.internal". make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -[ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -Scanning dependencies of target nclextra -[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/depend.internal". -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gauss.cpp -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -Scanning dependencies of target sprng -[ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -[ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/alignment.c -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c +[ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +[ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/avxLikelihood.c -[ 7%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -[ 8%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +[ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c +[ 8%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelfma.cpp -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 9%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/alignment.c +[ 10%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreeavx.cpp -Scanning dependencies of target whtest -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build -[ 9%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o +[ 11%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelsse.cpp -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 9%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -[ 10%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c -cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp -[ 11%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c In file included from /build/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 11%] Linking CXX static library libvectorclass.a +cd /build/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gaussinv.cpp -[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gausspdf.cpp -[ 13%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp -[ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +[ 13%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/makeseed.c -[ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/bipartitionList.c -[ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 13%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/memory.c -[ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gausspdf.cpp +[ 14%] Built target vectorclass +[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c +[ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c +[ 17%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/bipartitionList.c +[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c +[ 18%] Linking CXX static library libgsl.a +cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c In file included from /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -1156,46 +1214,33 @@ /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 15%] Linking CXX static library libgsl.a -[ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c -cd /build/iqtree-1.6.12+dfsg/build.omp/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 -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 17%] Built target gsl -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/vectorclass /build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +[ 18%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/checkid.c -In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: +In file included from /build/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". -Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 18%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/vectorclass/instrset_detect.cpp -[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c -In file included from /build/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: +[ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp +In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp -[ 20%] Linking C static library libsprng.a +[ 18%] Built target gsl +[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c +[ 19%] Linking C static library libsprng.a cd /build/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.omp' +[ 20%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c +[ 20%] Built target sprng In file included from /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1213,7 +1258,6 @@ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ -/usr/bin/ranlib libsprng.a /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -1226,35 +1270,12 @@ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 20%] Built target sprng -[ 20%] Linking CXX static library libvectorclass.a -cd /build/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 20%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c -cd /build/iqtree-1.6.12+dfsg/build.omp/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-1.6.12+dfsg/build.omp' -[ 20%] Built target vectorclass -[ 21%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c -[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp -[ 23%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c -[ 23%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.c -[ 24%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c -[ 25%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +[ 21%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hardware.c /build/iqtree-1.6.12+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.12+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1271,25 +1292,20 @@ /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ -[ 26%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +[ 21%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hash.c -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 27%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +[ 23%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/lexer.c -[ 28%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp -[ 28%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 23%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/makenewzGenericSpecial.c -[ 29%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 24%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/models.c +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c In file included from /build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1307,38 +1323,24 @@ /build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ +[ 25%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newick.c In file included from /build/iqtree-1.6.12+dfsg/pll/models.c:53: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp -[ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newick.c -[ 30%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.omp/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-1.6.12+dfsg/build.omp' In file included from /build/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 30%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 31%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +[ 26%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newviewGenericSpecial.c -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/depend.internal". -Scanning dependencies of target utils -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 32%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c +[ 28%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/genericParallelization.c +[ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1367,110 +1369,124 @@ /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ -[ 33%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/genericParallelization.c In file included from /build/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp -[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp -[ 34%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/optimizeModel.c -[ 35%] Linking C static library libpllavx.a +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp +[ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c +[ 30%] Linking C static library libpllavx.a cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.omp/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-1.6.12+dfsg/build.omp' -[ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp +[ 30%] Built target pllavx +[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp +[ 31%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/optimizeModel.c +[ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c In file included from /build/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 35%] Built target pllavx -[ 36%] Linking CXX static library libwhtest.a -[ 36%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp -cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp -/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-1.6.12+dfsg/build.omp' -[ 37%] Built target whtest -[ 38%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 32%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/parsePartition.c +[ 32%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/queue.c +[ 33%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp -[ 38%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/queue.c -[ 39%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +[ 34%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 34%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 35%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/randomTree.c +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/depend.internal". +Scanning dependencies of target utils +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 35%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/recom.c +[ 36%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/recom.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/recom.c -[ 40%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c +[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 37%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c +[ 38%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c In file included from /build/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 41%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c -[ 42%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp +[ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp +[ 38%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/ssort.c In file included from /build/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp -[ 43%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/ssort.c -[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp -[ 45%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +[ 39%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp +[ 40%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/stack.c -[ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 40%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 46%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp +[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp +[ 42%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/trash.c In file included from /build/iqtree-1.6.12+dfsg/pll/trash.c:48: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 46%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +[ 42%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/treeIO.c +[ 43%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c In file included from /build/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/stoprule.cpp -[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -1533,51 +1549,70 @@ /build/iqtree-1.6.12+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp +[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp +[ 46%] Linking CXX static library libwhtest.a +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp +/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-1.6.12+dfsg/build.omp' +[ 46%] Built target whtest +[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsstring.cpp -[ 49%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/tools.cpp -[ 49%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp -[ 50%] Linking CXX static library libnclextra.a -[ 51%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +[ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp +[ 48%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/MPIHelper.cpp -cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/checkpoint.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/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 -[ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp /usr/bin/ranlib libnclextra.a +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 52%] Built target nclextra +[ 49%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pda /build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/depend.internal". +[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/circularnetwork.cpp -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstoken.cpp -[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstreesblock.cpp -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/greedy.cpp -[ 55%] Linking C static library libpll.a +[ 50%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/circularnetwork.cpp +[ 51%] Linking C static library libpll.a cd /build/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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 libpll.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 51%] Built target pll +[ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +[ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/stoprule.cpp +[ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstreesblock.cpp +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/tools.cpp +[ 52%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp +[ 53%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/checkpoint.cpp +[ 54%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/greedy.cpp +[ 55%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/MPIHelper.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/gurobiwrapper.cpp -[ 56%] Built target pll [ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/hashsplitset.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o @@ -1592,23 +1627,17 @@ cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/splitset.cpp [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/lpwrapper.c -[ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopd.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/graph.cpp -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtree.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp -[ 64%] Linking CXX static library libncl.a +[ 61%] Linking CXX static library libncl.a +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopd.cpp cd /build/iqtree-1.6.12+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 /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 64%] Built target ncl +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/graph.cpp +[ 62%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/alignment /build/iqtree-1.6.12+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= @@ -1618,23 +1647,29 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/pattern.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtree.cpp +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignment.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignmentpairwise.cpp -[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/maalignment.cpp +[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignment.cpp [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwise.cpp -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp /build/iqtree-1.6.12+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 2925 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp [ 68%] Linking CXX static library libutils.a cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 @@ -1651,36 +1686,24 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 68%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmarkov.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o +[ 69%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmarkov.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelbin.cpp -[ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modeldna.cpp -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactory.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelprotein.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactory.cpp +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelset.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelsubst.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodel.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 142 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 149 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 156 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 163 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1702,7 +1725,8 @@ /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -1715,20 +1739,17 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: -/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); +/build/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 240 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: +[ 73%] Linking CXX static library libpda.a +cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -1741,13 +1762,13 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 240 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ +cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.omp' +[ 73%] Built target pda +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategamma.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelset.h:23, from /build/iqtree-1.6.12+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1775,16 +1796,33 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodelplen.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategamma.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 142 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 149 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 156 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 163 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategammainvar.cpp -[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterogeneity.cpp -[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateinvar.cpp /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ @@ -1797,13 +1835,10 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ -[ 75%] Linking CXX static library libpda.a -cd /build/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.omp' -[ 75%] Built target pda +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterogeneity.cpp +[ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o @@ -1824,6 +1859,8 @@ cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmixture.cpp +[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelunrest.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -1838,10 +1875,10 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelunrest.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: +[ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelliemarkov.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelcodon.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -1854,17 +1891,10 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -[ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelliemarkov.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelcodon.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomo.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -1877,10 +1907,13 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomo.cpp -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomomixture.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { + | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -1920,6 +1953,8 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomomixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, @@ -1998,13 +2033,6 @@ /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' [ 84%] Built target alignment -[ 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-1.6.12+dfsg/build.omp' -[ 84%] Built target kernelfma [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 @@ -2019,6 +2047,13 @@ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' [ 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-1.6.12+dfsg/build.omp' +[ 84%] Built target kernelfma [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -2035,40 +2070,37 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o +[ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.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/candidateset.cpp.o -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/iqtree.cpp -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/matree.cpp +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/constrainttree.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/candidateset.cpp +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/iqtree.cpp +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/matree.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mexttree.cpp -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtreeset.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/node.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonode.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonodemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertree.cpp cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertreeplen.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotree.cpp -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreemixlen.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: +In file included from /build/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2081,12 +2113,8 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreepars.cpp -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/quartet.cpp +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -2101,9 +2129,24 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreepars.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/quartet.cpp +/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] + 1202 | } + | ^ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/supernode.cpp -In file included from /build/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/tinatree.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/parstree.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, + from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2116,14 +2159,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/tinatree.cpp -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/parstree.cpp -/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] - 1202 | } - | ^ In file included from /build/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -2154,20 +2189,20 @@ make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/main.cpp -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o [ 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-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phylotesting.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/obsolete/parsmultistate.cpp +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/main.cpp /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2180,15 +2215,19 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2201,18 +2240,14 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(SeqType)': /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] 164 | } @@ -2228,7 +2263,7 @@ # 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" VERBOSE=1 + cd build.serial && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.12+dfsg/build.serial//CMakeFiles/progress.marks @@ -2241,174 +2276,183 @@ make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/gsl /build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/ncl /build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.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 make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.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-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/nclextra /build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/sprng /build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/vectorclass /build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/depend.internal". +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend Dependee "/build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/depend.internal". +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend Dependee "/build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/nclextra /build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= Scanning dependencies of target gsl -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/depend.internal". -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/depend.internal". -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/depend.internal". +Scanning dependencies of target lbfgsb +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend Dependee "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/depend.internal". -Scanning dependencies of target whtest +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/sprng /build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/vectorclass /build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= +make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build Scanning dependencies of target ncl +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' Dependee "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/depend.internal". make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". -Scanning dependencies of target nclextra -Scanning dependencies of target vectorclass -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". -make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/depend.internal". Scanning dependencies of target pllavx -Scanning dependencies of target lbfgsb -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' Dependee "/build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/depend.internal". -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +Scanning dependencies of target kernelfma +Scanning dependencies of target kernelsse make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +Scanning dependencies of target nclextra +Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -Scanning dependencies of target kernelavx -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/depend.internal". make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -Scanning dependencies of target sprng -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/binomial_tpe.cpp -[ 2%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -Scanning dependencies of target kernelsse +Scanning dependencies of target pll +[ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -Scanning dependencies of target pll -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build +cd /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/binomial_tpe.cpp +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 3%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o +[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". +Scanning dependencies of target vectorclass cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/multinomial.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -[ 3%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +Scanning dependencies of target whtest [ 5%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -[ 6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 7%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp +[ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelfma.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c -[ 7%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp +[ 6%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/pow_int.cpp -[ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gauss.cpp +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelsse.cpp +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o +[ 7%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/avxLikelihood.c +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreeavx.cpp +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +[ 9%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/alignment.c -[ 9%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +[ 10%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c +[ 10%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c +[ 11%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/vectorclass/instrset_detect.cpp -[ 10%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreeavx.cpp -[ 11%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelsse.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gauss.cpp [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gaussinv.cpp -[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +[ 13%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/makeseed.c +[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gausspdf.cpp -[ 13%] Linking CXX static library libvectorclass.a +[ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp +[ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/memory.c +[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp +[ 15%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.12+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/makeseed.c +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o /usr/bin/ranlib libvectorclass.a +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 14%] Built target vectorclass -[ 15%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o -[ 15%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/bipartitionList.c -[ 16%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -[ 17%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/memory.c -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c [ 17%] Linking CXX static library libgsl.a +cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +[ 17%] 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 +[ 18%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o In file included from /build/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c +/usr/bin/ranlib libgsl.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 18%] Built target gsl +[ 18%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/bipartitionList.c +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp +[ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2420,52 +2464,43 @@ /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c -cd /build/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 -[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.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 -[ 19%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c [ 19%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/checkid.c -[ 19%] Built target gsl -[ 19%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c -[ 20%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c -In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: -/build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ -[ 21%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c -[ 23%] Linking C static library libsprng.a +[ 20%] Linking C static library libsprng.a cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: +cd /build/iqtree-1.6.12+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 +[ 21%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c +/usr/bin/ranlib libsprng.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 21%] Built target sprng +[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp +In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 23%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:29: -/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': -/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' - 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); - | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' - 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); - | ^~~~~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c -cd /build/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp +[ 22%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c +[ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp +[ 24%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp +[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp +[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c +[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.c +[ 26%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2495,10 +2530,35 @@ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ -/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 +[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsstring.cpp +[ 29%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp +cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' -[ 23%] Built target sprng +[ 29%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/depend.internal". +Scanning dependencies of target utils +[ 29%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 30%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp +[ 31%] Linking C static library libpllavx.a +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); @@ -2506,38 +2566,50 @@ /build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp -[ 25%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp -[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp -[ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp -[ 27%] Building C object pll/CMakeFiles/pll.dir/hardware.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-1.6.12+dfsg/build.serial' +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstoken.cpp +[ 32%] Built target pllavx +[ 33%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c +In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: +/build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ +In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:29: +/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': +/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' + 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); + | ^~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' + 1768 | 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-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hardware.c /build/iqtree-1.6.12+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.12+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ -[ 27%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +[ 34%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstreesblock.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hash.c -[ 28%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +[ 34%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp +[ 35%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/lexer.c -[ 28%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 36%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp +[ 36%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/makenewzGenericSpecial.c -[ 29%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 37%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/models.c -[ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newick.c -[ 30%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newviewGenericSpecial.c -[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp -In file included from /build/iqtree-1.6.12+dfsg/pll/models.c:53: -/build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined - 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); - | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -2549,20 +2621,30 @@ /build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ -In file included from /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: +/build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': +/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] + 39 | #define rax_posix_memalign posix_memalign +/build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' + 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); + | ^~~~~~~~~~~~~~~~~~ +[ 37%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp +In file included from /build/iqtree-1.6.12+dfsg/pll/models.c:53: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 37%] Building C object pll/CMakeFiles/pll.dir/newick.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newick.c In file included from /build/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': -/build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] - 39 | #define rax_posix_memalign posix_memalign -/build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' - 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); - | ^~~~~~~~~~~~~~~~~~ +[ 38%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newviewGenericSpecial.c +In file included from /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: +/build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined + 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); + | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -2575,6 +2657,8 @@ /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ +[ 39%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/genericParallelization.c /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -2587,134 +2671,101 @@ /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ -[ 31%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/genericParallelization.c +[ 39%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/optimizeModel.c +[ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp -[ 33%] Linking C static library libpllavx.a -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -[ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp -cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' -[ 33%] Built target pllavx -[ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp -[ 34%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp -[ 35%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp -cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' -[ 36%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/depend.internal". -Scanning dependencies of target utils -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/optimizeModel.c -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp -[ 37%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp -[ 38%] Linking CXX static library libwhtest.a -cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' +[ 41%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 38%] Built target whtest -[ 38%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp -[ 39%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp +[ 42%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 39%] Building C object pll/CMakeFiles/pll.dir/queue.c.o -[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsstring.cpp +[ 42%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/stoprule.cpp +[ 43%] Linking CXX static library libwhtest.a +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 +[ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/queue.c -[ 41%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp -[ 42%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +/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-1.6.12+dfsg/build.serial' +[ 43%] Built target whtest +[ 44%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/tools.cpp +[ 45%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +[ 45%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/recom.c -[ 43%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c In file included from /build/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 46%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c +[ 47%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c In file included from /build/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 44%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c -[ 44%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +[ 47%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/ssort.c In file included from /build/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 45%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +[ 48%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/stack.c -[ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 48%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/topologies.c -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp +[ 49%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/trash.c In file included from /build/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstoken.cpp -[ 47%] Building C object pll/CMakeFiles/pll.dir/trash.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/trash.c +[ 49%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/treeIO.c In file included from /build/iqtree-1.6.12+dfsg/pll/trash.c:48: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstreesblock.cpp -[ 47%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/treeIO.c -[ 48%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c In file included from /build/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 50%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c +[ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp +[ 51%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/checkpoint.cpp +[ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/MPIHelper.cpp +[ 53%] Linking CXX static library libnclextra.a In file included from /build/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-1.6.12+dfsg/pll/utils.c: In function 'initializePartitionData': @@ -2773,34 +2824,11 @@ /build/iqtree-1.6.12+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp -[ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp -[ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/stoprule.cpp -[ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/tools.cpp -[ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp -[ 51%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/checkpoint.cpp -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/MPIHelper.cpp -[ 53%] Linking C static library libpll.a -cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.serial' -[ 53%] Built target pll -[ 54%] Linking CXX static library libnclextra.a -cd /build/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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 /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 54%] Built target nclextra +[ 53%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pda /build/iqtree-1.6.12+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= @@ -2810,37 +2838,50 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +[ 53%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/circularnetwork.cpp -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +[ 54%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/greedy.cpp -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o +[ 55%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/gurobiwrapper.cpp +[ 55%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/hashsplitset.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdnetwork.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pruning.cpp +[ 57%] Linking C static library libpll.a +cd /build/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+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 [ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/split.cpp +/usr/bin/ranlib libpll.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 58%] Built target pll [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/splitgraph.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/splitset.cpp [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/lpwrapper.c -[ 61%] Linking CXX static library libncl.a -cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -[ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o +[ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopd.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/graph.cpp +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtree.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp +[ 63%] Linking CXX static library libncl.a +cd /build/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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 -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/graph.cpp /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 62%] Built target ncl +[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp +[ 64%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/alignment /build/iqtree-1.6.12+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= @@ -2850,14 +2891,8 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/pattern.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtree.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignment.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o @@ -2866,19 +2901,19 @@ cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/maalignment.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignment.cpp -[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwise.cpp /build/iqtree-1.6.12+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 2925 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ -[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp -[ 68%] Linking CXX static library libutils.a +[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwise.cpp +[ 67%] Linking CXX static library libutils.a cd /build/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.serial/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-1.6.12+dfsg/build.serial' +[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' @@ -2897,14 +2932,8 @@ cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactory.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelprotein.cpp -[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelset.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelsubst.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2917,13 +2946,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 240 | void ModelDNA::readRates(string str) throw(const char*) { - | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -2937,10 +2959,36 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelprotein.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 142 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 149 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 156 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 163 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 240 | void ModelDNA::readRates(string str) throw(const char*) { + | ^~~~~ +[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelset.cpp +[ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelsubst.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodel.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -2953,6 +3001,30 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1052 | void ModelMarkov::readRates(string str) throw(const char*) { + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1081 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { + | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.h:23, @@ -2992,43 +3064,6 @@ | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategamma.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 142 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 149 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 156 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 163 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: -/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1052 | void ModelMarkov::readRates(string str) throw(const char*) { - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1081 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { - | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategammainvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o @@ -3039,27 +3074,21 @@ cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratemeyerhaeseler.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratekategory.cpp -[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratefree.cpp -[ 77%] Linking CXX static library libpda.a +[ 76%] Linking CXX static library libpda.a cd /build/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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 +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o /usr/bin/ranlib libpda.a +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratekategory.cpp make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' [ 77%] Built target pda +[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterotachy.cpp -[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterotachyinvar.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelcodon.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3074,12 +3103,20 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterotachyinvar.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelcodon.cpp +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelliemarkov.cpp +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3094,8 +3131,8 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomo.cpp +[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3117,8 +3154,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ -[ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomomixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: @@ -3146,8 +3181,9 @@ /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelunrest.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, + from /build/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3160,9 +3196,13 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, +In file included from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelunrest.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3175,11 +3215,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, @@ -3202,7 +3237,8 @@ /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp:12: +In file included from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3215,8 +3251,7 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -3236,6 +3271,13 @@ /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' [ 84%] Built target alignment +[ 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 +/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +/usr/bin/ranlib libkernelavx.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 84%] Built target kernelavx [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 @@ -3250,13 +3292,6 @@ /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.12+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 -/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -/usr/bin/ranlib libkernelavx.a -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 84%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -3273,38 +3308,36 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o +[ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o +[ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/constrainttree.cpp -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/candidateset.cpp -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o -[ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/matree.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/iqtree.cpp -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/matree.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/memslot.cpp -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtree.cpp -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mexttree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtree.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtreeset.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/ncbitree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/node.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonode.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonodemixlen.cpp -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertree.cpp -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/ncbitree.cpp +[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotree.cpp -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -3318,22 +3351,12 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 142 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 149 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 156 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 163 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ +[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreemixlen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreepars.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -3348,20 +3371,18 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/tinatree.cpp +[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/parstree.cpp /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] 1202 | } | ^ -[ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -3375,6 +3396,20 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, + from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 142 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 149 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 156 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 163 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -3391,20 +3426,20 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/main.cpp -/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp +[ 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-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phylotesting.cpp -[ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/obsolete/parsmultistate.cpp -/build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl - | ^~~~~~~~ +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp +/usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/build/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phylotesting.cpp /build/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ +/build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl + | ^~~~~~~~ In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -3466,7 +3501,7 @@ # 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" VERBOSE=1 + cd build.mpi && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.12+dfsg/build.mpi//CMakeFiles/progress.marks @@ -3475,160 +3510,172 @@ 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 -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/gsl /build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/ncl /build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= -make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= +make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= -make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/depend.internal". -Scanning dependencies of target gsl make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/sprng /build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/whtest /build/iqtree-1.6.12+dfsg/build.mpi/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-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/depend.internal". -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/depend.internal". -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -Scanning dependencies of target lbfgsb Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/depend.internal". Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/depend.internal". -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/depend.internal". +Scanning dependencies of target gsl +Scanning dependencies of target vectorclass +Scanning dependencies of target lbfgsb +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +Scanning dependencies of target sprng make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build -Scanning dependencies of target ncl +Scanning dependencies of target pllavx +Scanning dependencies of target nclextra make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -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/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/depend.internal". -Scanning dependencies of target kernelfma +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/depend.internal". make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/whtest /build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= -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 +[ 1%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o +Scanning dependencies of target ncl +[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o Scanning dependencies of target kernelavx -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/vectorclass/instrset_detect.cpp make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/binomial_tpe.cpp -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/depend.internal". -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build -Scanning dependencies of target pllavx -Scanning dependencies of target kernelsse -[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp +[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/multinomial.cpp +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/pow_int.cpp +[ 4%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +Scanning dependencies of target kernelfma +Scanning dependencies of target kernelsse +make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gauss.cpp -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -[ 4%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/pow_int.cpp -[ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelfma.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/depend.internal". -[ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +[ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gausspdf.cpp -[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gaussinv.cpp -[ 8%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreeavx.cpp -[ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp -[ 9%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -[ 9%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelsse.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/avxLikelihood.c -[ 10%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp -Scanning dependencies of target pll +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gauss.cpp Scanning dependencies of target whtest +[ 4%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/avxLikelihood.c +[ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o +[ 6%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreeavx.cpp +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 11%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o -[ 12%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/alignment.c -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/sprng /build/iqtree-1.6.12+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]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/depend.internal". -Scanning dependencies of target sprng -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". +[ 7%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelfma.cpp +Scanning dependencies of target pll +[ 8%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/depend.internal". -Scanning dependencies of target vectorclass make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/mpdablock.cpp +[ 10%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/alignment.c +[ 11%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen.c +[ 11%] Linking CXX static library libvectorclass.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake +[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gaussinv.cpp +/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o +/usr/bin/ranlib libvectorclass.a In file included from /build/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 12%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c -[ 13%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -[ 13%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/vectorclass/instrset_detect.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/lcg64.c -[ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 13%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/makeseed.c +[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o +[ 14%] Built target vectorclass +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -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-1.6.12+dfsg/gsl/gausspdf.cpp +[ 14%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/eigen_sym.c +[ 14%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp +[ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsblock.cpp +[ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/memory.c [ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/bipartitionList.c -[ 14%] Linking CXX static library libgsl.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +[ 15%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o +[ 16%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c In file included from /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3640,52 +3687,31 @@ /build/iqtree-1.6.12+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ -[ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/memory.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 -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 14%] Built target gsl -[ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/store.c -[ 16%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c -[ 16%] Linking CXX static library libvectorclass.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake -[ 16%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/checkid.c -[ 17%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluateGenericSpecial.c -cd /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 -[ 17%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c -In file included from /build/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: +In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -/usr/bin/ranlib libvectorclass.a -[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp -[ 18%] Built target vectorclass -In file included from /build/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: +[ 16%] Linking CXX static library libgsl.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 +In file included from /build/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 19%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -[ 20%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hardware.c -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c -[ 21%] Linking C static library libsprng.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake -[ 22%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +/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-1.6.12+dfsg/build.mpi' +[ 16%] Built target gsl +[ 16%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c +[ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/primes-lcg64.c +[ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxscharactersblock.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c In file included from /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] @@ -3699,10 +3725,6 @@ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/pll/hardware.c: In function 'pll_probe_cpu': -/build/iqtree-1.6.12+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 93 | fscanf (fd, "%d", &id); - | ^~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.12+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign @@ -3715,10 +3737,33 @@ /build/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ +[ 18%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/sprng/checkid.c +[ 19%] Linking C static library libsprng.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake +[ 20%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/random.c +cd /build/iqtree-1.6.12+dfsg/build.mpi/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-1.6.12+dfsg/build.mpi' -[ 22%] Built target sprng +[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c +[ 21%] Built target sprng +[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp +[ 23%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/fastDNAparsimony.c +[ 23%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.c +[ 24%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hardware.c +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c +/build/iqtree-1.6.12+dfsg/pll/hardware.c: In function 'pll_probe_cpu': +/build/iqtree-1.6.12+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 93 | fscanf (fd, "%d", &id); + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3735,20 +3780,25 @@ /build/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ -[ 22%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +[ 25%] Building C object pll/CMakeFiles/pll.dir/hash.c.o +[ 25%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/hash.c -[ 23%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function 'ReadData': +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 205 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] + 221 | fscanf ( ifp, "%c", &c ); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 26%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/lexer.c -[ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdatablock.cpp -[ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda.c -[ 25%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o +[ 27%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp +[ 27%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/makenewzGenericSpecial.c -[ 26%] Building C object pll/CMakeFiles/pll.dir/models.c.o +[ 28%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/models.c -[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3770,29 +3820,20 @@ /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o -[ 27%] Building C object pll/CMakeFiles/pll.dir/newick.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest.c +[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp +[ 28%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newick.c -[ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_sub.c In file included from /build/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function 'ReadData': -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 205 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/build/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] - 221 | fscanf ( ifp, "%c", &c ); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o +[ 29%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/newviewGenericSpecial.c -[ 29%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/whtest/whtest_wrapper.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/genericParallelization.c +[ 31%] Linking C static library libpllavx.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3821,101 +3862,105 @@ /build/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ +cd /build/iqtree-1.6.12+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 +[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o +[ 33%] Linking CXX static library liblbfgsb.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp +cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake +/usr/bin/ranlib libpllavx.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp -[ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp -[ 31%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o +[ 33%] Built target pllavx +/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o +/usr/bin/ranlib liblbfgsb.a +[ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp +[ 33%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/depend.internal". +Scanning dependencies of target utils +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 34%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp +[ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp +[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp +[ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/optimizeModel.c +[ 37%] Linking CXX static library libwhtest.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+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-1.6.12+dfsg/build.mpi' In file included from /build/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 32%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +[ 37%] Built target whtest +[ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp +[ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o +[ 38%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/parsePartition.c -[ 33%] Linking CXX static library liblbfgsb.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -/usr/bin/ranlib liblbfgsb.a -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 33%] Built target lbfgsb -[ 34%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/randomTree.c -[ 34%] Building C object pll/CMakeFiles/pll.dir/queue.c.o +[ 38%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/queue.c -[ 35%] Linking CXX static library libwhtest.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 -[ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -/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 -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancedatum.cpp -/usr/bin/ranlib libwhtest.a -[ 35%] Building C object pll/CMakeFiles/pll.dir/recom.c.o +[ 39%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp +[ 40%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/recom.c -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsdistancesblock.cpp -[ 36%] Built target whtest -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 37%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/depend.internal". In file included from /build/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -Scanning dependencies of target utils -[ 38%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 39%] Linking C static library libpllavx.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake -[ 40%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/eigendecomposition.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 +[ 41%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/restartHashTable.c In file included from /build/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o -/usr/bin/ranlib libpllavx.a -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 40%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/ssort.c +[ 42%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/searchAlgo.c +[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 40%] Built target pllavx -[ 40%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp -[ 41%] Building C object pll/CMakeFiles/pll.dir/stack.c.o +[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp +[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsstring.cpp +[ 44%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/ssort.c +[ 45%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/stack.c -[ 41%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o +[ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/topologies.c -[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msetsblock.cpp -[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsemptyblock.cpp -[ 42%] Building C object pll/CMakeFiles/pll.dir/trash.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/trash.c In file included from /build/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined @@ -3925,14 +3970,36 @@ /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ -[ 42%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o +[ 46%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/treeIO.c -[ 43%] Building C object pll/CMakeFiles/pll.dir/utils.c.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c In file included from /build/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ +[ 47%] Linking CXX static library libnclextra.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.mpi/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 +/usr/bin/ranlib libnclextra.a +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 47%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/depend.internal". +Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/depend.internal". +Scanning dependencies of target pda +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 48%] Building C object pll/CMakeFiles/pll.dir/utils.c.o +[ 48%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pll/utils.c +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/circularnetwork.cpp +[ 48%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/gzstream.cpp +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp In file included from /build/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-1.6.12+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); @@ -3995,68 +4062,36 @@ /build/iqtree-1.6.12+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ -[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsexception.cpp -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsreader.cpp -[ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxssetreader.cpp -[ 46%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/optimization.cpp -[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxsstring.cpp -[ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp -[ 47%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o +[ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/stoprule.cpp -[ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstaxablock.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstoken.cpp -[ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o +[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/ncl/nxstreesblock.cpp -[ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/msplitsblock.cpp -[ 49%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/nclextra/modelsblock.cpp -[ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o +[ 51%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/greedy.cpp +[ 52%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/gurobiwrapper.cpp +[ 53%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/tools.cpp -[ 51%] Linking C static library libpll.a +[ 53%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp +[ 54%] Linking C static library libpll.a cd /build/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+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 utils/CMakeFiles/utils.dir/pllnni.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/pllnni.cpp /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 51%] Built target pll -[ 52%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o +[ 54%] Built target pll +[ 55%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/checkpoint.cpp -[ 53%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o +[ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/utils/MPIHelper.cpp -[ 54%] Linking CXX static library libnclextra.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.mpi/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 -/usr/bin/ranlib libnclextra.a -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 54%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/depend.internal". -Dependee "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/depend.internal". -Scanning dependencies of target pda -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 54%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/circularnetwork.cpp -[ 55%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/greedy.cpp -[ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/gurobiwrapper.cpp -[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o +[ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/hashsplitset.cpp +[ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdnetwork.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pruning.cpp @@ -4070,17 +4105,21 @@ cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/lpwrapper.c [ 60%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopd.cpp -[ 61%] Linking CXX static library libncl.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/graph.cpp -[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o +[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtree.cpp +[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp +[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp +[ 64%] Linking CXX static library libncl.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake +cd /build/iqtree-1.6.12+dfsg/build.mpi/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-1.6.12+dfsg/build.mpi' -[ 62%] Built target ncl +[ 64%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/alignment /build/iqtree-1.6.12+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= @@ -4090,17 +4129,13 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/pattern.cpp -[ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/pdtreeset.cpp -[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+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-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignment.cpp +[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/pattern.cpp [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignmentpairwise.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/alignmentpairwise.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/maalignment.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/alignment/superalignment.cpp @@ -4132,22 +4167,23 @@ [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelbin.cpp -[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modeldna.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactory.cpp +[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactory.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelsubst.cpp -[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o +[ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodel.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/partitionmodelplen.cpp -[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategamma.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: +[ 73%] Linking CXX static library libpda.a +cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake +In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4160,18 +4196,20 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: +In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { + | ^~~~~ +cd /build/iqtree-1.6.12+dfsg/build.mpi/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-1.6.12+dfsg/build.mpi' +[ 73%] Built target pda +[ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategamma.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4193,7 +4231,8 @@ /build/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 240 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4206,8 +4245,8 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelset.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4220,15 +4259,7 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: -/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 69 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelset.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelset.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4241,8 +4272,19 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelbin.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: +/build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 69 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4255,6 +4297,10 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategammainvar.cpp +[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterogeneity.cpp /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ @@ -4267,19 +4313,8 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ -[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rategammainvar.cpp -[ 74%] Linking CXX static library libpda.a -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake -cd /build/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 -[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -/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 -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o -/usr/bin/ranlib libpda.a cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateinvar.cpp -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 75%] Built target pda [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o @@ -4296,8 +4331,6 @@ cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelcodon.cpp -[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4312,16 +4345,34 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ +[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelunrest.cpp +In file included from /build/iqtree-1.6.12+dfsg/model/modelcodon.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 142 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 149 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 156 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 163 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelpomomixture.cpp +[ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4343,6 +4394,20 @@ /build/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/model/modelunrest.h:11, + from /build/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 142 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 149 | virtual void readRates(string str) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 156 | virtual void readStateFreq(istream &in) throw(const char*); + | ^~~~~ +/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 163 | virtual void readStateFreq(string str) throw(const char*); + | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); @@ -4368,8 +4433,10 @@ /build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelcodon.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: +In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, + from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, + from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4382,22 +4449,12 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/model/modelfactorymixlen.cpp -In file included from /build/iqtree-1.6.12+dfsg/model/modelunrest.h:11, - from /build/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 142 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 149 | virtual void readRates(string str) throw(const char*); +In file included from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, + from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, + from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: +/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 156 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 163 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: @@ -4431,28 +4488,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modeldna.h:23, - from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 142 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 149 | virtual void readRates(string str) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 156 | virtual void readStateFreq(istream &in) throw(const char*); - | ^~~~~ -/build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 163 | virtual void readStateFreq(string str) throw(const char*); - | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/model/modelpomo.h:4, - from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, - from /build/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: -/build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 91 | virtual void readRates(string str) throw(const char*); - | ^~~~~ In file included from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] @@ -4481,20 +4516,20 @@ /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' [ 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 [ 84%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake -/usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -/usr/bin/ranlib libkernelfma.a /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 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-1.6.12+dfsg/build.mpi' [ 84%] Built target kernelfma -[ 84%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 @@ -4512,34 +4547,34 @@ make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o -[ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o -[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o +[ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o -[ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/candidateset.cpp +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o +[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o +[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/constrainttree.cpp +cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/iqtree.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/matree.cpp +cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mexttree.cpp -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o -[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtree.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/mtreeset.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/node.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonode.cpp -[ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o +[ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylonodemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertree.cpp -cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreemixlen.cpp @@ -4558,8 +4593,12 @@ | ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreepars.cpp +[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp +[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o +cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/quartet.cpp In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: + from /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4572,18 +4611,18 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/phylotreesse.cpp -[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o -cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/tree/parstree.cpp +/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': +/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] + 1202 | } + | ^ In file included from /build/iqtree-1.6.12+dfsg/model/modelmixture.h:13, - from /build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: + from /build/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4609,10 +4648,6 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': -/build/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] - 1202 | } - | ^ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 @@ -4629,21 +4664,21 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.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-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phylotesting.cpp -/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp +[ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o +[ 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-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/main.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/obsolete/parsmultistate.cpp -/build/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; - | ^~~~~~~~ +[ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o +[ 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-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phyloanalysis.cpp +/usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-1.6.12+dfsg=. -fstack-protector-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-1.6.12+dfsg/main/phylotesting.cpp /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: +/build/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; + | ^~~~~~~~ +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4656,15 +4691,19 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: +In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: +/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] + 78 | virtual void readRates(istream &in) throw(const char*, string); + | ^~~~~ +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ @@ -4677,18 +4716,14 @@ /build/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: +In file included from /build/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ -In file included from /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: -/build/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] - 78 | virtual void readRates(istream &in) throw(const char*, string); - | ^~~~~ /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(SeqType)': /build/iqtree-1.6.12+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] 164 | } @@ -4712,18 +4747,18 @@ echo 'time /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo' >> example.short time sh example.short Executing tests using /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp ... -+ time /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy ++ /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy IQ-TREE multicore version 1.6.12 for Linux 64-bit built Dec 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos15-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -Seed: 111137 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Mon Jan 30 07:19:06 2023 -Kernel: AVX - 1 threads (16 CPU cores detected) +Seed: 16571 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Wed Dec 29 03:08:35 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 @@ -4778,274 +4813,266 @@ **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) -Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.007 seconds +Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.005 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 11922.053 85 24014.106 24063.166 24349.910 - 2 JC+I 11670.098 86 23512.196 23562.580 23851.952 - 3 JC+G4 11397.457 86 22966.913 23017.297 23306.668 - 4 JC+I+G4 11377.914 87 22929.828 22981.558 23273.534 - 5 JC+R2 11495.491 87 23164.983 23216.713 23508.689 - 6 JC+R3 11383.389 89 22944.779 22999.269 23296.386 - 7 JC+R4 11375.074 91 22932.148 22989.490 23291.656 - 8 JC+R5 11374.936 93 22935.872 22996.161 23303.282 - 14 F81+F 11925.120 88 24026.240 24079.338 24373.896 - 15 F81+F+I 11669.928 89 23517.857 23572.347 23869.464 - 16 F81+F+G4 11392.582 89 22963.164 23017.654 23314.771 - 17 F81+F+I+G4 11373.266 90 22926.532 22982.436 23282.089 - 18 F81+F+R2 11492.696 90 23165.391 23221.296 23520.949 - 19 F81+F+R3 11376.535 92 22937.070 22995.874 23300.529 - 20 F81+F+R4 11370.242 94 22928.485 22990.284 23299.845 - 21 F81+F+R5 11370.230 96 22932.460 22997.352 23311.722 - 27 K2P 11885.411 86 23942.823 23993.207 24282.578 - 28 K2P+I 11632.618 87 23439.235 23490.965 23782.941 - 29 K2P+G4 11354.302 87 22882.603 22934.333 23226.309 - 30 K2P+I+G4 11335.382 88 22846.765 22899.863 23194.421 - 31 K2P+R2 11455.552 88 23087.105 23140.203 23434.761 - 32 K2P+R3 11338.400 90 22856.799 22912.704 23212.357 - 33 K2P+R4 11332.013 92 22848.026 22906.830 23211.485 - 34 K2P+R5 11331.908 94 22851.816 22913.615 23223.176 - 40 HKY+F 11887.872 89 23953.744 24008.234 24305.352 - 41 HKY+F+I 11630.990 90 23441.979 23497.884 23797.537 - 42 HKY+F+G4 11346.777 90 22873.554 22929.458 23229.112 - 43 HKY+F+I+G4 11328.136 91 22838.271 22895.614 23197.780 - 44 HKY+F+R2 11450.686 91 23083.372 23140.714 23442.880 - 45 HKY+F+R3 11331.908 93 22849.815 22910.105 23217.225 - 46 HKY+F+R4 11324.691 95 22839.381 22902.714 23214.692 - 47 HKY+F+R5 11324.615 97 22843.229 22909.705 23226.442 - 53 TNe 11884.866 87 23943.731 23995.461 24287.437 - 54 TNe+I 11627.490 88 23430.979 23484.078 23778.636 - 55 TNe+G4 11353.253 88 22882.507 22935.605 23230.163 - 56 TNe+I+G4 11333.703 89 22845.406 22899.896 23197.014 - 57 TNe+R2 11454.606 89 23087.212 23141.702 23438.819 - 58 TNe+R3 11335.265 91 22852.530 22909.873 23212.039 - 59 TNe+R4 11329.414 93 22844.828 22905.118 23212.238 - 66 TN+F 11887.255 90 23954.511 24010.415 24310.069 - 67 TN+F+I 11625.151 91 23432.302 23489.644 23791.810 - 68 TN+F+G4 11345.175 91 22872.349 22929.692 23231.858 - 69 TN+F+I+G4 11325.776 92 22835.552 22894.356 23199.011 - 70 TN+F+R2 11449.303 92 23082.605 23141.410 23446.065 - 71 TN+F+R3 11327.919 94 22843.838 22905.638 23215.199 - 72 TN+F+R4 11321.332 96 22834.664 22899.556 23213.926 - 73 TN+F+R5 11321.234 98 22838.469 22906.553 23225.632 - 79 K3P 11869.150 87 23912.301 23964.030 24256.007 - 80 K3P+I 11615.829 88 23407.658 23460.757 23755.315 - 81 K3P+G4 11341.005 88 22858.010 22911.109 23205.667 - 82 K3P+I+G4 11321.395 89 22820.790 22875.280 23172.397 - 83 K3P+R2 11438.583 89 23055.166 23109.656 23406.774 - 84 K3P+R3 11323.690 91 22829.381 22886.723 23188.889 - 85 K3P+R4 11317.585 93 22821.170 22881.460 23188.580 - 86 K3P+R5 11317.545 95 22825.090 22888.424 23200.401 - 92 K3Pu+F 11871.724 90 23923.448 23979.352 24279.006 - 93 K3Pu+F+I 11614.345 91 23410.691 23468.033 23770.199 - 94 K3Pu+F+G4 11334.222 91 22850.445 22907.787 23209.953 - 95 K3Pu+F+I+G4 11314.856 92 22813.711 22872.515 23177.170 - 96 K3Pu+F+R2 11434.133 92 23052.266 23111.070 23415.725 - 97 K3Pu+F+R3 11317.897 94 22823.795 22885.594 23195.155 - 98 K3Pu+F+R4 11310.931 96 22813.862 22878.754 23193.123 - 99 K3Pu+F+R5 11310.866 98 22817.732 22885.816 23204.895 -105 TPM2+F 11887.629 90 23955.259 24011.163 24310.817 -106 TPM2+F+I 11630.566 91 23443.132 23500.474 23802.640 -107 TPM2+F+G4 11346.584 91 22875.168 22932.511 23234.677 -108 TPM2+F+I+G4 11327.974 92 22839.947 22898.751 23203.406 -109 TPM2+F+R2 11450.663 92 23085.327 23144.131 23448.786 -110 TPM2+F+R3 11331.120 94 22850.240 22912.040 23221.601 -111 TPM2+F+R4 11323.892 96 22839.784 22904.676 23219.046 -112 TPM2+F+R5 11323.831 98 22843.663 22911.747 23230.826 -118 TPM2u+F 11887.629 90 23955.259 24011.163 24310.817 -119 TPM2u+F+I 11630.566 91 23443.132 23500.474 23802.640 -120 TPM2u+F+G4 11346.584 91 22875.168 22932.511 23234.677 -121 TPM2u+F+I+G4 11327.975 92 22839.951 22898.755 23203.410 -122 TPM2u+F+R2 11450.668 92 23085.336 23144.140 23448.795 -123 TPM2u+F+R3 11331.039 94 22850.078 22911.877 23221.439 -124 TPM2u+F+R4 11323.775 96 22839.549 22904.441 23218.811 -125 TPM2u+F+R5 11323.722 98 22843.444 22911.529 23230.607 -131 TPM3+F 11857.311 90 23894.622 23950.526 24250.180 -132 TPM3+F+I 11619.663 91 23421.326 23478.669 23780.835 -133 TPM3+F+G4 11343.300 91 22868.599 22925.942 23228.108 -134 TPM3+F+I+G4 11325.262 92 22834.523 22893.327 23197.982 -135 TPM3+F+R2 11445.092 92 23074.184 23132.988 23437.643 -136 TPM3+F+R3 11326.617 94 22841.234 22903.033 23212.594 -137 TPM3+F+R4 11320.619 96 22833.238 22898.130 23212.500 -138 TPM3+F+R5 11320.586 98 22837.171 22905.256 23224.334 -144 TPM3u+F 11857.311 90 23894.622 23950.527 24250.180 -145 TPM3u+F+I 11619.663 91 23421.326 23478.669 23780.835 -146 TPM3u+F+G4 11343.300 91 22868.600 22925.942 23228.108 -147 TPM3u+F+I+G4 11325.262 92 22834.523 22893.327 23197.982 -148 TPM3u+F+R2 11445.078 92 23074.155 23132.960 23437.615 -149 TPM3u+F+R3 11326.566 94 22841.132 22902.931 23212.493 -150 TPM3u+F+R4 11320.545 96 22833.090 22897.982 23212.352 -151 TPM3u+F+R5 11320.514 98 22837.028 22905.112 23224.191 -157 TIMe 11868.595 88 23913.191 23966.289 24260.847 -158 TIMe+I 11610.673 89 23399.345 23453.835 23750.952 -159 TIMe+G4 11339.949 89 22857.897 22912.387 23209.504 -160 TIMe+I+G4 11319.701 90 22819.401 22875.305 23174.959 -161 TIMe+R2 11437.661 90 23055.323 23111.227 23410.881 -162 TIMe+R3 11320.297 92 22824.593 22883.397 23188.052 -163 TIMe+R4 11314.756 94 22817.513 22879.312 23188.873 -170 TIM+F 11871.101 91 23924.203 23981.545 24283.711 -171 TIM+F+I 11608.492 92 23400.985 23459.789 23764.444 -172 TIM+F+G4 11332.627 92 22849.255 22908.059 23212.714 -173 TIM+F+I+G4 11312.491 93 22810.982 22871.271 23178.392 -174 TIM+F+R2 11432.722 93 23051.444 23111.734 23418.854 -175 TIM+F+R3 11313.705 95 22817.409 22880.742 23192.720 -176 TIM+F+R4 11307.327 97 22808.653 22875.129 23191.866 -177 TIM+F+R5 11307.286 99 22812.573 22882.291 23203.686 -183 TIM2e 11884.544 88 23945.088 23998.187 24292.745 -184 TIM2e+I 11626.988 89 23431.976 23486.466 23783.583 -185 TIM2e+G4 11353.168 89 22884.335 22938.825 23235.943 -186 TIM2e+I+G4 11333.645 90 22847.290 22903.194 23202.847 -187 TIM2e+R2 11454.537 90 23089.073 23144.978 23444.631 -188 TIM2e+R3 11334.234 92 22852.469 22911.273 23215.928 -189 TIM2e+R4 11328.372 94 22844.744 22906.544 23216.105 -196 TIM2+F 11887.019 91 23956.038 24013.380 24315.546 -197 TIM2+F+I 11624.757 92 23433.513 23492.317 23796.972 -198 TIM2+F+G4 11344.988 92 22873.975 22932.779 23237.434 -199 TIM2+F+I+G4 11325.631 93 22837.261 22897.551 23204.671 -200 TIM2+F+R2 11449.281 93 23084.563 23144.852 23451.973 -201 TIM2+F+R3 11326.978 95 22843.956 22907.289 23219.267 -202 TIM2+F+R4 11320.287 97 22834.574 22901.050 23217.787 -203 TIM2+F+R5 11320.253 99 22838.506 22908.225 23229.620 -209 TIM3e 11845.980 88 23867.959 23921.057 24215.616 -210 TIM3e+I 11610.685 89 23399.370 23453.860 23750.978 -211 TIM3e+G4 11345.837 89 22869.674 22924.163 23221.281 -212 TIM3e+I+G4 11327.240 90 22834.479 22890.384 23190.037 -213 TIM3e+R2 11444.135 90 23068.271 23124.175 23423.829 -214 TIM3e+R3 11325.588 92 22835.175 22893.980 23198.635 -215 TIM3e+R4 11321.463 94 22830.926 22892.725 23202.286 -222 TIM3+F 11856.514 91 23895.028 23952.370 24254.536 -223 TIM3+F+I 11613.804 92 23411.607 23470.411 23775.066 -224 TIM3+F+G4 11341.601 92 22867.203 22926.007 23230.662 -225 TIM3+F+I+G4 11322.828 93 22831.656 22891.946 23199.066 -226 TIM3+F+R2 11443.717 93 23073.434 23133.724 23440.844 -227 TIM3+F+R3 11322.510 95 22835.019 22898.352 23210.330 -228 TIM3+F+R4 11317.044 97 22828.089 22894.564 23211.301 -235 TVMe 11829.850 89 23837.701 23892.191 24189.308 -236 TVMe+I 11598.594 90 23377.189 23433.093 23732.746 -237 TVMe+G4 11331.950 90 22843.900 22899.804 23199.458 -238 TVMe+I+G4 11313.539 91 22809.078 22866.420 23168.586 -239 TVMe+R2 11427.798 91 23037.596 23094.938 23397.104 -240 TVMe+R3 11313.234 93 22812.468 22872.758 23179.878 -241 TVMe+R4 11309.029 95 22808.057 22871.390 23183.368 -248 TVM+F 11840.607 92 23865.214 23924.018 24228.673 -249 TVM+F+I 11602.624 93 23391.247 23451.537 23758.657 -250 TVM+F+G4 11328.857 93 22843.714 22904.004 23211.124 -251 TVM+F+I+G4 11310.273 94 22808.547 22870.346 23179.907 -252 TVM+F+R2 11428.008 94 23044.017 23105.816 23415.377 -253 TVM+F+R3 11311.487 96 22814.975 22879.867 23194.237 -254 TVM+F+R4 11305.972 98 22807.943 22876.027 23195.106 -261 SYM 11829.108 90 23838.215 23894.120 24193.773 -262 SYM+I 11593.389 91 23368.777 23426.120 23728.286 -263 SYM+G4 11330.677 91 22843.353 22900.696 23202.862 -264 SYM+I+G4 11311.665 92 22807.330 22866.134 23170.789 -265 SYM+R2 11426.736 92 23037.471 23096.275 23400.930 -266 SYM+R3 11309.966 94 22807.932 22869.731 23179.292 -267 SYM+R4 11306.392 96 22804.784 22869.676 23184.046 -274 GTR+F 11839.783 93 23865.566 23925.856 24232.976 -275 GTR+F+I 11596.710 94 23381.420 23443.219 23752.780 -276 GTR+F+G4 11327.141 94 22842.282 22904.081 23213.643 -277 GTR+F+I+G4 11307.855 95 22805.711 22869.044 23181.022 -278 GTR+F+R2 11426.668 95 23043.336 23106.669 23418.647 -279 GTR+F+R3 11307.495 97 22808.989 22875.465 23192.202 -280 GTR+F+R4 11302.673 99 22803.345 22873.063 23194.459 -Akaike Information Criterion: GTR+F+R4 -Corrected Akaike Information Criterion: SYM+I+G4 + 1 JC 11927.542 85 24025.084 24074.144 24360.888 + 2 JC+I 11670.792 86 23513.585 23563.968 23853.340 + 3 JC+G4 11359.348 86 22890.696 22941.080 23230.451 + 4 JC+I+G4 11342.266 87 22858.533 22910.262 23202.239 + 5 JC+R2 11465.115 87 23104.231 23155.961 23447.937 + 6 JC+R3 11347.652 89 22873.304 22927.793 23224.911 + 7 JC+R4 11340.576 91 22863.153 22920.495 23222.661 + 8 JC+R5 11340.356 93 22866.711 22927.001 23234.121 + 14 F81+F 11930.572 88 24037.145 24090.243 24384.801 + 15 F81+F+I 11670.828 89 23519.657 23574.147 23871.264 + 16 F81+F+G4 11353.600 89 22885.200 22939.690 23236.807 + 17 F81+F+I+G4 11336.774 90 22853.549 22909.453 23209.107 + 18 F81+F+R2 11461.946 90 23103.891 23159.796 23459.449 + 19 F81+F+R3 11341.185 92 22866.370 22925.174 23229.829 + 20 F81+F+R4 11334.918 94 22857.836 22919.636 23229.197 + 21 F81+F+R5 11334.735 96 22861.471 22926.363 23240.733 + 27 K2P 11881.920 86 23935.841 23986.225 24275.596 + 28 K2P+I 11625.664 87 23425.329 23477.059 23769.035 + 29 K2P+G4 11311.816 87 22797.633 22849.362 23141.338 + 30 K2P+I+G4 11295.083 88 22766.165 22819.263 23113.822 + 31 K2P+R2 11420.186 88 23016.373 23069.471 23364.029 + 32 K2P+R3 11298.967 90 22777.934 22833.838 23133.492 + 33 K2P+R4 11292.822 92 22769.645 22828.449 23133.104 + 34 K2P+R5 11292.716 94 22773.432 22835.231 23144.792 + 40 HKY+F 11884.029 89 23946.059 24000.548 24297.666 + 41 HKY+F+I 11623.907 90 23427.814 23483.718 23783.371 + 42 HKY+F+G4 11303.282 90 22786.565 22842.469 23142.122 + 43 HKY+F+I+G4 11286.757 91 22755.514 22812.856 23115.022 + 44 HKY+F+R2 11414.585 91 23011.171 23068.513 23370.679 + 45 HKY+F+R3 11291.396 93 22768.792 22829.082 23136.202 + 46 HKY+F+R4 11284.342 95 22758.684 22822.017 23133.995 + 47 HKY+F+R5 11284.238 97 22762.476 22828.951 23145.688 + 53 TNe 11880.127 87 23934.253 23985.983 24277.959 + 54 TNe+I 11617.520 88 23411.040 23464.139 23758.697 + 55 TNe+G4 11309.908 88 22795.816 22848.914 23143.472 + 56 TNe+I+G4 11292.346 89 22762.692 22817.182 23114.299 + 57 TNe+R2 11418.179 89 23014.358 23068.847 23365.965 + 58 TNe+R3 11294.801 91 22771.602 22828.944 23131.110 + 59 TNe+R4 11289.178 93 22764.356 22824.645 23131.766 + 66 TN+F 11882.090 90 23944.180 24000.085 24299.738 + 67 TN+F+I 11614.790 91 23411.580 23468.923 23771.089 + 68 TN+F+G4 11300.640 91 22783.281 22840.623 23142.789 + 69 TN+F+I+G4 11283.143 92 22750.287 22809.091 23113.746 + 70 TN+F+R2 11411.863 92 23007.726 23066.530 23371.185 + 71 TN+F+R3 11286.298 94 22760.596 22822.395 23131.956 + 72 TN+F+R4 11279.852 96 22751.705 22816.597 23130.966 + 73 TN+F+R5 11279.750 98 22755.500 22823.584 23142.663 + 79 K3P 11870.594 87 23915.188 23966.917 24258.893 + 80 K3P+I 11613.125 88 23402.250 23455.348 23749.906 + 81 K3P+G4 11301.802 88 22779.603 22832.701 23127.260 + 82 K3P+I+G4 11284.479 89 22746.958 22801.448 23098.565 + 83 K3P+R2 11406.784 89 22991.568 23046.058 23343.175 + 84 K3P+R3 11287.725 91 22757.449 22814.792 23116.958 + 85 K3P+R4 11281.637 93 22749.273 22809.563 23116.683 + 86 K3P+R5 11281.590 95 22753.180 22816.513 23128.491 + 92 K3Pu+F 11872.986 90 23925.973 23981.877 24281.531 + 93 K3Pu+F+I 11611.578 91 23405.157 23462.499 23764.665 + 94 K3Pu+F+G4 11293.905 91 22769.810 22827.153 23129.319 + 95 K3Pu+F+I+G4 11276.791 92 22737.582 22796.386 23101.041 + 96 K3Pu+F+R2 11401.654 92 22987.308 23046.112 23350.767 + 97 K3Pu+F+R3 11280.917 94 22749.834 22811.634 23121.195 + 98 K3Pu+F+R4 11273.862 96 22739.723 22804.615 23118.985 + 99 K3Pu+F+R5 11273.797 98 22743.594 22811.679 23130.757 +105 TPM2+F 11884.006 90 23948.013 24003.917 24303.571 +106 TPM2+F+I 11623.782 91 23429.564 23486.906 23789.072 +107 TPM2+F+G4 11302.139 91 22786.278 22843.620 23145.786 +108 TPM2+F+I+G4 11285.802 92 22755.605 22814.409 23119.064 +109 TPM2+F+R2 11414.326 92 23012.652 23071.456 23376.111 +110 TPM2+F+R3 11289.896 94 22767.792 22829.591 23139.152 +111 TPM2+F+R4 11282.920 96 22757.841 22822.733 23137.102 +112 TPM2+F+R5 11282.887 98 22761.775 22829.859 23148.937 +118 TPM2u+F 11883.999 90 23947.999 24003.903 24303.557 +119 TPM2u+F+I 11623.783 91 23429.565 23486.908 23789.074 +120 TPM2u+F+G4 11302.139 91 22786.278 22843.620 23145.786 +121 TPM2u+F+I+G4 11285.803 92 22755.606 22814.410 23119.065 +122 TPM2u+F+R2 11414.332 92 23012.664 23071.469 23376.123 +123 TPM2u+F+R3 11289.843 94 22767.685 22829.485 23139.046 +124 TPM2u+F+R4 11282.804 96 22757.608 22822.500 23136.870 +125 TPM2u+F+R5 11282.752 98 22761.505 22829.589 23148.668 +131 TPM3+F 11850.105 90 23880.209 23936.114 24235.767 +132 TPM3+F+I 11610.448 91 23402.895 23460.238 23762.404 +133 TPM3+F+G4 11299.536 91 22781.072 22838.414 23140.580 +134 TPM3+F+I+G4 11283.712 92 22751.424 22810.228 23114.883 +135 TPM3+F+R2 11408.626 92 23001.252 23060.056 23364.711 +136 TPM3+F+R3 11286.122 94 22760.244 22822.043 23131.605 +137 TPM3+F+R4 11280.076 96 22752.152 22817.044 23131.414 +138 TPM3+F+R5 11280.042 98 22756.084 22824.168 23143.247 +144 TPM3u+F 11850.106 90 23880.212 23936.116 24235.770 +145 TPM3u+F+I 11610.448 91 23402.895 23460.238 23762.404 +146 TPM3u+F+G4 11299.536 91 22781.073 22838.415 23140.581 +147 TPM3u+F+I+G4 11283.712 92 22751.425 22810.229 23114.884 +148 TPM3u+F+R2 11408.615 92 23001.229 23060.034 23364.689 +149 TPM3u+F+R3 11286.092 94 22760.184 22821.983 23131.544 +150 TPM3u+F+R4 11279.998 96 22751.997 22816.889 23131.259 +151 TPM3u+F+R5 11279.966 98 22755.932 22824.016 23143.095 +157 TIMe 11868.866 88 23913.733 23966.831 24261.390 +158 TIMe+I 11605.100 89 23388.199 23442.689 23739.806 +159 TIMe+G4 11299.969 89 22777.938 22832.428 23129.545 +160 TIMe+I+G4 11281.829 90 22743.658 22799.563 23099.216 +161 TIMe+R2 11405.094 90 22990.188 23046.093 23345.746 +162 TIMe+R3 11283.561 92 22751.122 22809.926 23114.581 +163 TIMe+R4 11277.934 94 22743.868 22805.667 23115.228 +170 TIM+F 11871.107 91 23924.214 23981.557 24283.723 +171 TIM+F+I 11602.595 92 23389.191 23447.995 23752.650 +172 TIM+F+G4 11291.350 92 22766.700 22825.504 23130.159 +173 TIM+F+I+G4 11273.271 93 22732.542 22792.831 23099.951 +174 TIM+F+R2 11399.153 93 22984.307 23044.596 23351.717 +175 TIM+F+R3 11275.789 95 22741.577 22804.911 23116.888 +176 TIM+F+R4 11269.203 97 22732.406 22798.882 23115.619 +177 TIM+F+R5 11269.162 99 22736.323 22806.041 23127.437 +183 TIM2e 11880.064 88 23936.127 23989.226 24283.784 +184 TIM2e+I 11617.349 89 23412.699 23467.189 23764.306 +185 TIM2e+G4 11309.072 89 22796.144 22850.633 23147.751 +186 TIM2e+I+G4 11291.704 90 22763.408 22819.312 23118.966 +187 TIM2e+R2 11418.055 90 23016.111 23072.015 23371.669 +188 TIM2e+R3 11293.443 92 22770.886 22829.691 23134.346 +189 TIM2e+R4 11287.733 94 22763.466 22825.265 23134.826 +196 TIM2+F 11882.064 91 23946.128 24003.470 24305.636 +197 TIM2+F+I 11614.680 92 23413.359 23472.163 23776.818 +198 TIM2+F+G4 11299.528 92 22783.057 22841.861 23146.516 +199 TIM2+F+I+G4 11282.253 93 22750.506 22810.795 23117.915 +200 TIM2+F+R2 11411.683 93 23009.365 23069.655 23376.775 +201 TIM2+F+R3 11284.790 95 22759.580 22822.914 23134.891 +202 TIM2+F+R4 11278.222 97 22750.445 22816.921 23133.657 +203 TIM2+F+R5 11278.190 99 22754.380 22824.099 23145.494 +209 TIM3e 11836.871 88 23849.742 23902.841 24197.399 +210 TIM3e+I 11598.092 89 23374.185 23428.674 23725.792 +211 TIM3e+G4 11302.094 89 22782.188 22836.678 23133.796 +212 TIM3e+I+G4 11285.601 90 22751.202 22807.107 23106.760 +213 TIM3e+R2 11407.386 90 22994.772 23050.677 23350.330 +214 TIM3e+R3 11285.210 92 22754.420 22813.224 23117.879 +215 TIM3e+R4 11281.017 94 22750.034 22811.833 23121.394 +222 TIM3+F 11847.887 91 23877.774 23935.116 24237.282 +223 TIM3+F+I 11601.409 92 23386.818 23445.622 23750.277 +224 TIM3+F+G4 11296.726 92 22777.452 22836.256 23140.911 +225 TIM3+F+I+G4 11279.974 93 22745.948 22806.237 23113.357 +226 TIM3+F+R2 11406.082 93 22998.164 23058.453 23365.573 +227 TIM3+F+R3 11280.913 95 22751.826 22815.159 23127.137 +228 TIM3+F+R4 11275.370 97 22744.740 22811.215 23127.952 +235 TVMe 11826.556 89 23831.113 23885.602 24182.720 +236 TVMe+I 11592.904 90 23365.807 23421.712 23721.365 +237 TVMe+G4 11291.225 90 22762.451 22818.355 23118.009 +238 TVMe+I+G4 11275.287 91 22732.574 22789.917 23092.083 +239 TVMe+R2 11394.816 91 22971.632 23028.974 23331.140 +240 TVMe+R3 11276.244 93 22738.488 22798.777 23105.898 +241 TVMe+R4 11271.891 95 22733.783 22797.116 23109.094 +248 TVM+F 11837.949 92 23859.897 23918.702 24223.357 +249 TVM+F+I 11597.441 93 23380.883 23441.172 23748.293 +250 TVM+F+G4 11286.843 93 22759.686 22819.976 23127.096 +251 TVM+F+I+G4 11270.761 94 22729.521 22791.321 23100.882 +252 TVM+F+R2 11394.360 94 22976.720 23038.520 23348.081 +253 TVM+F+R3 11273.233 96 22738.466 22803.358 23117.728 +254 TVM+F+R4 11267.520 98 22731.039 22799.123 23118.202 +261 SYM 11824.533 90 23829.066 23884.971 24184.624 +262 SYM+I 11584.972 91 23351.944 23409.286 23711.452 +263 SYM+G4 11289.155 91 22760.311 22817.653 23119.819 +264 SYM+I+G4 11272.485 92 22728.970 22787.774 23092.429 +265 SYM+R2 11393.010 92 22970.020 23028.824 23333.479 +266 SYM+R3 11272.191 94 22732.382 22794.181 23103.742 +267 SYM+R4 11268.530 96 22729.060 22793.952 23108.321 +274 GTR+F 11835.789 93 23857.578 23917.868 24224.988 +275 GTR+F+I 11588.515 94 23365.030 23426.829 23736.390 +276 GTR+F+G4 11284.164 94 22756.328 22818.128 23127.689 +277 GTR+F+I+G4 11267.202 95 22724.404 22787.738 23099.715 +278 GTR+F+R2 11392.044 95 22974.088 23037.422 23349.399 +279 GTR+F+R3 11268.292 97 22730.583 22797.059 23113.795 +280 GTR+F+R4 11263.339 99 22724.679 22794.397 23115.792 +Akaike Information Criterion: GTR+F+I+G4 +Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 38.252 seconds (0h:0m:38s) -Wall-clock time for ModelFinder: 50.857 seconds (0h:0m:50s) +CPU time for ModelFinder: 32.101 seconds (0h:0m:32s) +Wall-clock time for ModelFinder: 32.231 seconds (0h:0m:32s) 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, 0.975 / LogL: -11331.956 -Init pinv, alpha: 0.012, 1.000 / Estimate: 0.087, 1.676 / LogL: -11313.524 -Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.677 / LogL: -11313.524 -Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.675 / LogL: -11313.524 -Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.678 / LogL: -11313.523 -Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.674 / LogL: -11313.524 -Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.677 / LogL: -11313.523 -Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.679 / LogL: -11313.521 -Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.682 / LogL: -11313.521 -Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.682 / LogL: -11313.521 -Optimal pinv,alpha: 0.087, 1.682 / LogL: -11313.521 +Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.949 / LogL: -11291.225 +Init pinv, alpha: 0.012, 1.000 / Estimate: 0.084, 1.531 / LogL: -11275.302 +Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.535 / LogL: -11275.290 +Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.532 / LogL: -11275.291 +Init pinv, alpha: 0.046, 1.000 / Estimate: 0.084, 1.537 / LogL: -11275.288 +Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.533 / LogL: -11275.290 +Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.537 / LogL: -11275.286 +Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.540 / LogL: -11275.285 +Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.544 / LogL: -11275.285 +Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.544 / LogL: -11275.286 +Optimal pinv,alpha: 0.085, 1.540 / LogL: -11275.285 -Parameters optimization took 4.063 sec -Computing ML distances based on estimated model parameters... 0.022 sec +Parameters optimization took 2.833 sec +Computing ML distances based on estimated model parameters... 0.019 sec Computing BIONJ tree... -0.006 seconds -Log-likelihood of BIONJ tree: -11270.546 +0.001 seconds +Log-likelihood of BIONJ tree: -11271.297 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 0.881 second -Computing log-likelihood of 98 initial trees ... 5.122 seconds -Current best score: -11241.114 +Generating 98 parsimony trees... 0.663 second +Computing log-likelihood of 98 initial trees ... 3.628 seconds +Current best score: -11248.191 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11225.739 +BETTER TREE FOUND at iteration 1: -11231.895 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 4: -11224.864 -Iteration 10 / LogL: -11227.888 / Time: 0h:0m:16s -Iteration 20 / LogL: -11225.673 / Time: 0h:0m:21s -Finish initializing candidate tree set (17) -Current best tree score: -11224.864 / CPU time: 17.684 +BETTER TREE FOUND at iteration 2: -11226.696 +Iteration 10 / LogL: -11244.684 / Time: 0h:0m:10s +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 15: -11225.466 +Iteration 20 / LogL: -11231.385 / Time: 0h:0m:13s +Finish initializing candidate tree set (13) +Current best tree score: -11225.466 / CPU time: 10.300 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -11225.269 / Time: 0h:0m:27s (0h:1m:10s left) -Iteration 40 / LogL: -11225.734 / Time: 0h:0m:33s (0h:0m:54s left) -Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 49: -11224.095 -Iteration 50 / LogL: -11225.121 / Time: 0h:0m:41s (0h:1m:24s left) -Iteration 60 / LogL: -11225.434 / Time: 0h:0m:48s (0h:1m:13s left) -UPDATE BEST LOG-LIKELIHOOD: -11224.090 -Iteration 70 / LogL: -11224.411 / Time: 0h:0m:54s (0h:1m:2s left) -Iteration 80 / LogL: -11225.331 / Time: 0h:0m:59s (0h:0m:52s left) -UPDATE BEST LOG-LIKELIHOOD: -11224.081 -Iteration 90 / LogL: -11224.092 / Time: 0h:1m:4s (0h:0m:42s left) -Iteration 100 / LogL: -11224.469 / Time: 0h:1m:9s (0h:0m:34s left) Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 106: -11223.037 +BETTER TREE FOUND at iteration 27: -11223.422 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 108: -11222.778 -Iteration 110 / LogL: -11224.683 / Time: 0h:1m:14s (0h:1m:6s left) -Iteration 120 / LogL: -11222.863 / Time: 0h:1m:19s (0h:0m:58s left) -Iteration 130 / LogL: -11222.815 / Time: 0h:1m:26s (0h:0m:52s left) -Iteration 140 / LogL: -11231.664 / Time: 0h:1m:33s (0h:0m:45s left) -Iteration 150 / LogL: -11222.807 / Time: 0h:1m:38s (0h:0m:38s left) -Iteration 160 / LogL: -11222.935 / Time: 0h:1m:45s (0h:0m:31s left) -Iteration 170 / LogL: -11222.923 / Time: 0h:1m:50s (0h:0m:24s left) -Iteration 180 / LogL: -11222.784 / Time: 0h:1m:55s (0h:0m:18s left) -Iteration 190 / LogL: -11223.660 / Time: 0h:2m:0s (0h:0m:11s left) -Iteration 200 / LogL: -11223.424 / Time: 0h:2m:6s (0h:0m:5s left) -TREE SEARCH COMPLETED AFTER 209 ITERATIONS / Time: 0h:2m:12s +BETTER TREE FOUND at iteration 30: -11222.785 +Iteration 30 / LogL: -11222.785 / Time: 0h:0m:18s (0h:1m:2s left) +BETTER TREE FOUND at iteration 37: -11222.783 +Iteration 40 / LogL: -11222.792 / Time: 0h:0m:22s (0h:0m:56s left) +Iteration 50 / LogL: -11226.300 / Time: 0h:0m:27s (0h:0m:48s left) +Iteration 60 / LogL: -11222.937 / Time: 0h:0m:31s (0h:0m:41s left) +Iteration 70 / LogL: -11222.913 / Time: 0h:0m:36s (0h:0m:35s left) +Iteration 80 / LogL: -11224.183 / Time: 0h:0m:40s (0h:0m:29s left) +Iteration 90 / LogL: -11224.016 / Time: 0h:0m:45s (0h:0m:23s left) +Iteration 100 / LogL: -11231.574 / Time: 0h:0m:49s (0h:0m:18s left) +Iteration 110 / LogL: -11224.186 / Time: 0h:0m:54s (0h:0m:13s left) +Iteration 120 / LogL: -11222.920 / Time: 0h:0m:58s (0h:0m:8s left) +Iteration 130 / LogL: -11223.263 / Time: 0h:1m:4s (0h:0m:3s left) +TREE SEARCH COMPLETED AFTER 138 ITERATIONS / Time: 0h:1m:7s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11222.778 +1. Initial log-likelihood: -11222.783 Optimal log-likelihood: -11222.773 -Rate parameters: A-C: 1.51936 A-G: 2.61516 A-T: 1.68157 C-G: 1.98467 C-T: 2.61516 G-T: 1.00000 +Rate parameters: A-C: 1.52011 A-G: 2.61098 A-T: 1.67219 C-G: 1.98141 C-T: 2.61098 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.083 -Gamma shape alpha: 1.528 -Parameters optimization took 1 rounds (0.086 sec) +Gamma shape alpha: 1.530 +Parameters optimization took 1 rounds (0.066 sec) BEST SCORE FOUND : -11222.773 Total tree length: 12.599 -Total number of iterations: 209 -CPU time used for tree search: 106.633 sec (0h:1m:46s) -Wall-clock time used for tree search: 128.072 sec (0h:2m:8s) -Total CPU time used: 110.180 sec (0h:1m:50s) -Total wall-clock time used: 132.404 sec (0h:2m:12s) +Total number of iterations: 138 +CPU time used for tree search: 64.229 sec (0h:1m:4s) +Wall-clock time used for tree search: 64.760 sec (0h:1m:4s) +Total CPU time used: 67.254 sec (0h:1m:7s) +Total wall-clock time used: 67.790 sec (0h:1m:7s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -5053,19 +5080,21 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Mon Jan 30 07:22:09 2023 -148.44user 1.12system 3:03.29elapsed 81%CPU (0avgtext+0avgdata 14480maxresident)k -0inputs+0outputs (0major+4684minor)pagefaults 0swaps -+ time /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo +Date and Time: Wed Dec 29 03:10:15 2021 + +real 1m40.044s +user 1m39.369s +sys 0m0.592s ++ /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo IQ-TREE multicore version 1.6.12 for Linux 64-bit built Dec 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. -Host: ionos15-amd64 (AVX, 47 GB RAM) +Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo -Seed: 407736 (Using SPRNG - Scalable Parallel Random Number Generator) -Time: Mon Jan 30 07:22:09 2023 -Kernel: AVX - 2 threads (16 CPU cores detected) +Seed: 61399 (Using SPRNG - Scalable Parallel Random Number Generator) +Time: Wed Dec 29 03:10:15 2021 +Kernel: AVX - 2 threads (15 CPU cores detected) Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences @@ -5124,254 +5153,275 @@ NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC - 1 JC 11922.053 85 24014.106 24063.166 24349.910 - 2 JC+I 11670.098 86 23512.196 23562.580 23851.952 - 3 JC+G4 11397.457 86 22966.913 23017.297 23306.668 - 4 JC+I+G4 11377.914 87 22929.828 22981.558 23273.534 - 5 JC+R2 11495.491 87 23164.983 23216.713 23508.689 - 6 JC+R3 11383.389 89 22944.779 22999.269 23296.386 - 7 JC+R4 11375.074 91 22932.148 22989.490 23291.656 - 8 JC+R5 11374.936 93 22935.872 22996.161 23303.282 - 14 F81+F 11925.120 88 24026.240 24079.338 24373.896 - 15 F81+F+I 11669.928 89 23517.857 23572.347 23869.464 - 16 F81+F+G4 11392.582 89 22963.164 23017.654 23314.771 - 17 F81+F+I+G4 11373.266 90 22926.532 22982.436 23282.089 - 18 F81+F+R2 11492.696 90 23165.391 23221.296 23520.949 - 19 F81+F+R3 11376.535 92 22937.070 22995.874 23300.529 - 20 F81+F+R4 11370.242 94 22928.485 22990.284 23299.845 - 21 F81+F+R5 11370.230 96 22932.460 22997.352 23311.722 - 27 K2P 11885.411 86 23942.823 23993.207 24282.578 - 28 K2P+I 11632.618 87 23439.235 23490.965 23782.941 - 29 K2P+G4 11354.302 87 22882.603 22934.333 23226.309 - 30 K2P+I+G4 11335.382 88 22846.765 22899.863 23194.421 - 31 K2P+R2 11455.552 88 23087.105 23140.203 23434.761 - 32 K2P+R3 11338.400 90 22856.799 22912.704 23212.357 - 33 K2P+R4 11332.013 92 22848.026 22906.830 23211.485 - 34 K2P+R5 11331.908 94 22851.816 22913.615 23223.176 - 40 HKY+F 11887.872 89 23953.744 24008.234 24305.352 - 41 HKY+F+I 11630.990 90 23441.979 23497.884 23797.537 - 42 HKY+F+G4 11346.777 90 22873.554 22929.458 23229.112 - 43 HKY+F+I+G4 11328.136 91 22838.271 22895.614 23197.780 - 44 HKY+F+R2 11450.686 91 23083.372 23140.714 23442.880 - 45 HKY+F+R3 11331.908 93 22849.815 22910.105 23217.225 - 46 HKY+F+R4 11324.691 95 22839.381 22902.714 23214.692 - 47 HKY+F+R5 11324.615 97 22843.229 22909.705 23226.442 - 53 TNe 11884.866 87 23943.731 23995.461 24287.437 - 54 TNe+I 11627.490 88 23430.979 23484.078 23778.636 - 55 TNe+G4 11353.253 88 22882.507 22935.605 23230.163 - 56 TNe+I+G4 11333.703 89 22845.406 22899.896 23197.014 - 57 TNe+R2 11454.606 89 23087.212 23141.702 23438.819 - 58 TNe+R3 11335.265 91 22852.530 22909.873 23212.039 - 59 TNe+R4 11329.414 93 22844.828 22905.118 23212.238 - 66 TN+F 11887.255 90 23954.511 24010.415 24310.069 - 67 TN+F+I 11625.151 91 23432.302 23489.644 23791.810 - 68 TN+F+G4 11345.175 91 22872.349 22929.692 23231.858 - 69 TN+F+I+G4 11325.776 92 22835.552 22894.356 23199.011 - 70 TN+F+R2 11449.303 92 23082.605 23141.410 23446.065 - 71 TN+F+R3 11327.919 94 22843.838 22905.638 23215.199 - 72 TN+F+R4 11321.332 96 22834.664 22899.556 23213.926 - 73 TN+F+R5 11321.234 98 22838.469 22906.553 23225.632 - 79 K3P 11869.150 87 23912.301 23964.030 24256.007 - 80 K3P+I 11615.829 88 23407.658 23460.757 23755.315 - 81 K3P+G4 11341.005 88 22858.010 22911.109 23205.667 - 82 K3P+I+G4 11321.395 89 22820.790 22875.280 23172.397 - 83 K3P+R2 11438.583 89 23055.166 23109.656 23406.774 - 84 K3P+R3 11323.690 91 22829.381 22886.723 23188.889 - 85 K3P+R4 11317.585 93 22821.170 22881.460 23188.580 - 86 K3P+R5 11317.545 95 22825.090 22888.424 23200.401 - 92 K3Pu+F 11871.724 90 23923.448 23979.352 24279.006 - 93 K3Pu+F+I 11614.345 91 23410.691 23468.033 23770.199 - 94 K3Pu+F+G4 11334.222 91 22850.445 22907.787 23209.953 - 95 K3Pu+F+I+G4 11314.856 92 22813.711 22872.515 23177.170 - 96 K3Pu+F+R2 11434.133 92 23052.266 23111.070 23415.725 - 97 K3Pu+F+R3 11317.897 94 22823.795 22885.594 23195.155 - 98 K3Pu+F+R4 11310.931 96 22813.862 22878.754 23193.123 - 99 K3Pu+F+R5 11310.866 98 22817.732 22885.816 23204.895 -105 TPM2+F 11887.629 90 23955.259 24011.163 24310.817 -106 TPM2+F+I 11630.566 91 23443.132 23500.474 23802.640 -107 TPM2+F+G4 11346.584 91 22875.168 22932.511 23234.677 -108 TPM2+F+I+G4 11327.974 92 22839.947 22898.751 23203.406 -109 TPM2+F+R2 11450.663 92 23085.327 23144.131 23448.786 -110 TPM2+F+R3 11331.120 94 22850.240 22912.040 23221.601 -111 TPM2+F+R4 11323.892 96 22839.784 22904.676 23219.046 -112 TPM2+F+R5 11323.831 98 22843.663 22911.747 23230.826 -118 TPM2u+F 11887.629 90 23955.259 24011.163 24310.817 -119 TPM2u+F+I 11630.566 91 23443.132 23500.474 23802.640 -120 TPM2u+F+G4 11346.584 91 22875.168 22932.511 23234.677 -121 TPM2u+F+I+G4 11327.975 92 22839.951 22898.755 23203.410 -122 TPM2u+F+R2 11450.668 92 23085.336 23144.140 23448.795 -123 TPM2u+F+R3 11331.039 94 22850.078 22911.877 23221.439 -124 TPM2u+F+R4 11323.775 96 22839.549 22904.441 23218.811 -125 TPM2u+F+R5 11323.722 98 22843.444 22911.529 23230.607 -131 TPM3+F 11857.311 90 23894.622 23950.526 24250.180 -132 TPM3+F+I 11619.663 91 23421.326 23478.669 23780.835 -133 TPM3+F+G4 11343.300 91 22868.599 22925.942 23228.108 -134 TPM3+F+I+G4 11325.262 92 22834.523 22893.327 23197.982 -135 TPM3+F+R2 11445.092 92 23074.184 23132.988 23437.643 -136 TPM3+F+R3 11326.617 94 22841.234 22903.033 23212.594 -137 TPM3+F+R4 11320.619 96 22833.238 22898.130 23212.500 -138 TPM3+F+R5 11320.586 98 22837.171 22905.256 23224.334 -144 TPM3u+F 11857.311 90 23894.622 23950.527 24250.180 -145 TPM3u+F+I 11619.663 91 23421.326 23478.669 23780.835 -146 TPM3u+F+G4 11343.300 91 22868.600 22925.942 23228.108 -147 TPM3u+F+I+G4 11325.262 92 22834.523 22893.327 23197.982 -148 TPM3u+F+R2 11445.078 92 23074.155 23132.960 23437.615 -149 TPM3u+F+R3 11326.566 94 22841.132 22902.931 23212.493 -150 TPM3u+F+R4 11320.545 96 22833.090 22897.982 23212.352 -151 TPM3u+F+R5 11320.514 98 22837.028 22905.112 23224.191 -157 TIMe 11868.595 88 23913.191 23966.289 24260.847 -158 TIMe+I 11610.673 89 23399.345 23453.835 23750.952 -159 TIMe+G4 11339.949 89 22857.897 22912.387 23209.504 -160 TIMe+I+G4 11319.701 90 22819.401 22875.305 23174.959 -161 TIMe+R2 11437.661 90 23055.323 23111.227 23410.881 -162 TIMe+R3 11320.297 92 22824.593 22883.397 23188.052 -163 TIMe+R4 11314.756 94 22817.513 22879.312 23188.873 -170 TIM+F 11871.101 91 23924.203 23981.545 24283.711 -171 TIM+F+I 11608.492 92 23400.985 23459.789 23764.444 -172 TIM+F+G4 11332.627 92 22849.255 22908.059 23212.714 -173 TIM+F+I+G4 11312.491 93 22810.982 22871.271 23178.392 -174 TIM+F+R2 11432.722 93 23051.444 23111.734 23418.854 -175 TIM+F+R3 11313.705 95 22817.409 22880.742 23192.720 -176 TIM+F+R4 11307.327 97 22808.653 22875.129 23191.866 -177 TIM+F+R5 11307.286 99 22812.572 22882.291 23203.686 -183 TIM2e 11884.544 88 23945.088 23998.187 24292.745 -184 TIM2e+I 11626.988 89 23431.976 23486.466 23783.583 -185 TIM2e+G4 11353.168 89 22884.335 22938.825 23235.943 -186 TIM2e+I+G4 11333.645 90 22847.290 22903.194 23202.847 -187 TIM2e+R2 11454.537 90 23089.073 23144.978 23444.631 -188 TIM2e+R3 11334.234 92 22852.469 22911.273 23215.928 -189 TIM2e+R4 11328.372 94 22844.744 22906.544 23216.105 -196 TIM2+F 11887.019 91 23956.038 24013.380 24315.546 -197 TIM2+F+I 11624.757 92 23433.513 23492.317 23796.972 -198 TIM2+F+G4 11344.988 92 22873.975 22932.779 23237.434 -199 TIM2+F+I+G4 11325.631 93 22837.261 22897.551 23204.671 -200 TIM2+F+R2 11449.281 93 23084.563 23144.852 23451.973 -201 TIM2+F+R3 11326.978 95 22843.956 22907.289 23219.267 -202 TIM2+F+R4 11320.287 97 22834.574 22901.050 23217.787 -203 TIM2+F+R5 11320.253 99 22838.506 22908.225 23229.620 -209 TIM3e 11845.980 88 23867.959 23921.057 24215.616 -210 TIM3e+I 11610.685 89 23399.370 23453.860 23750.978 -211 TIM3e+G4 11345.837 89 22869.674 22924.163 23221.281 -212 TIM3e+I+G4 11327.240 90 22834.479 22890.384 23190.037 -213 TIM3e+R2 11444.135 90 23068.271 23124.175 23423.829 -214 TIM3e+R3 11325.588 92 22835.175 22893.980 23198.635 -215 TIM3e+R4 11321.463 94 22830.926 22892.725 23202.286 -222 TIM3+F 11856.514 91 23895.028 23952.370 24254.536 -223 TIM3+F+I 11613.804 92 23411.607 23470.411 23775.066 -224 TIM3+F+G4 11341.601 92 22867.203 22926.007 23230.662 -225 TIM3+F+I+G4 11322.828 93 22831.656 22891.946 23199.066 -226 TIM3+F+R2 11443.717 93 23073.434 23133.724 23440.844 -227 TIM3+F+R3 11322.510 95 22835.019 22898.352 23210.330 -228 TIM3+F+R4 11317.044 97 22828.089 22894.564 23211.301 -235 TVMe 11829.850 89 23837.701 23892.191 24189.308 -236 TVMe+I 11598.594 90 23377.189 23433.093 23732.746 -237 TVMe+G4 11331.950 90 22843.900 22899.804 23199.458 -238 TVMe+I+G4 11313.539 91 22809.078 22866.420 23168.586 -239 TVMe+R2 11427.798 91 23037.596 23094.938 23397.104 -240 TVMe+R3 11313.234 93 22812.468 22872.758 23179.878 -241 TVMe+R4 11309.029 95 22808.057 22871.390 23183.368 -248 TVM+F 11840.607 92 23865.214 23924.018 24228.673 -249 TVM+F+I 11602.624 93 23391.247 23451.537 23758.657 -250 TVM+F+G4 11328.857 93 22843.714 22904.004 23211.124 -251 TVM+F+I+G4 11310.273 94 22808.547 22870.346 23179.907 -252 TVM+F+R2 11428.008 94 23044.017 23105.816 23415.377 -253 TVM+F+R3 11311.487 96 22814.975 22879.867 23194.237 -254 TVM+F+R4 11305.972 98 22807.943 22876.027 23195.106 -261 SYM 11829.108 90 23838.215 23894.120 24193.773 -262 SYM+I 11593.389 91 23368.777 23426.120 23728.286 -263 SYM+G4 11330.677 91 22843.353 22900.696 23202.862 -264 SYM+I+G4 11311.665 92 22807.330 22866.134 23170.789 -265 SYM+R2 11426.736 92 23037.471 23096.275 23400.930 -266 SYM+R3 11309.966 94 22807.932 22869.731 23179.292 -267 SYM+R4 11306.392 96 22804.784 22869.676 23184.046 -274 GTR+F 11839.783 93 23865.566 23925.856 24232.976 -275 GTR+F+I 11596.710 94 23381.420 23443.219 23752.780 -276 GTR+F+G4 11327.141 94 22842.282 22904.081 23213.643 -277 GTR+F+I+G4 11307.855 95 22805.711 22869.044 23181.022 -278 GTR+F+R2 11426.668 95 23043.336 23106.669 23418.647 -279 GTR+F+R3 11307.495 97 22808.989 22875.465 23192.202 -280 GTR+F+R4 11302.673 99 22803.345 22873.063 23194.459 -Akaike Information Criterion: GTR+F+R4 -Corrected Akaike Information Criterion: SYM+I+G4 + 1 JC 11927.542 85 24025.084 24074.144 24360.888 + 2 JC+I 11670.792 86 23513.585 23563.968 23853.340 + 3 JC+G4 11359.348 86 22890.696 22941.080 23230.451 + 4 JC+I+G4 11342.266 87 22858.533 22910.262 23202.239 + 5 JC+R2 11465.115 87 23104.231 23155.961 23447.937 + 6 JC+R3 11347.652 89 22873.304 22927.793 23224.911 + 7 JC+R4 11340.576 91 22863.153 22920.495 23222.661 + 8 JC+R5 11340.356 93 22866.711 22927.001 23234.121 + 14 F81+F 11930.572 88 24037.145 24090.243 24384.801 + 15 F81+F+I 11670.828 89 23519.657 23574.147 23871.264 + 16 F81+F+G4 11353.600 89 22885.200 22939.690 23236.807 + 17 F81+F+I+G4 11336.774 90 22853.549 22909.453 23209.107 + 18 F81+F+R2 11461.946 90 23103.891 23159.796 23459.449 + 19 F81+F+R3 11341.185 92 22866.370 22925.174 23229.829 + 20 F81+F+R4 11334.918 94 22857.836 22919.636 23229.197 + 21 F81+F+R5 11334.735 96 22861.471 22926.363 23240.733 + 27 K2P 11881.920 86 23935.841 23986.225 24275.596 + 28 K2P+I 11625.664 87 23425.329 23477.059 23769.035 + 29 K2P+G4 11311.816 87 22797.633 22849.362 23141.338 + 30 K2P+I+G4 11295.083 88 22766.165 22819.263 23113.822 + 31 K2P+R2 11420.186 88 23016.373 23069.471 23364.029 + 32 K2P+R3 11298.967 90 22777.934 22833.838 23133.492 + 33 K2P+R4 11292.822 92 22769.645 22828.449 23133.104 + 34 K2P+R5 11292.716 94 22773.432 22835.231 23144.792 + 40 HKY+F 11884.029 89 23946.059 24000.548 24297.666 + 41 HKY+F+I 11623.907 90 23427.814 23483.718 23783.371 + 42 HKY+F+G4 11303.282 90 22786.565 22842.469 23142.122 + 43 HKY+F+I+G4 11286.757 91 22755.514 22812.856 23115.022 + 44 HKY+F+R2 11414.585 91 23011.171 23068.513 23370.679 + 45 HKY+F+R3 11291.396 93 22768.792 22829.082 23136.202 + 46 HKY+F+R4 11284.342 95 22758.684 22822.017 23133.995 + 47 HKY+F+R5 11284.238 97 22762.476 22828.951 23145.688 + 53 TNe 11880.127 87 23934.253 23985.983 24277.959 + 54 TNe+I 11617.520 88 23411.040 23464.139 23758.697 + 55 TNe+G4 11309.908 88 22795.816 22848.914 23143.472 + 56 TNe+I+G4 11292.346 89 22762.692 22817.182 23114.299 + 57 TNe+R2 11418.179 89 23014.358 23068.847 23365.965 + 58 TNe+R3 11294.801 91 22771.602 22828.944 23131.110 + 59 TNe+R4 11289.178 93 22764.356 22824.645 23131.766 + 66 TN+F 11882.090 90 23944.180 24000.085 24299.738 + 67 TN+F+I 11614.790 91 23411.580 23468.923 23771.089 + 68 TN+F+G4 11300.640 91 22783.281 22840.623 23142.789 + 69 TN+F+I+G4 11283.143 92 22750.287 22809.091 23113.746 + 70 TN+F+R2 11411.863 92 23007.726 23066.530 23371.185 + 71 TN+F+R3 11286.298 94 22760.596 22822.395 23131.956 + 72 TN+F+R4 11279.852 96 22751.705 22816.597 23130.966 + 73 TN+F+R5 11279.750 98 22755.500 22823.584 23142.663 + 79 K3P 11870.594 87 23915.188 23966.917 24258.893 + 80 K3P+I 11613.125 88 23402.250 23455.348 23749.906 + 81 K3P+G4 11301.802 88 22779.603 22832.701 23127.260 + 82 K3P+I+G4 11284.479 89 22746.958 22801.448 23098.565 + 83 K3P+R2 11406.784 89 22991.568 23046.058 23343.175 + 84 K3P+R3 11287.725 91 22757.449 22814.792 23116.958 + 85 K3P+R4 11281.637 93 22749.273 22809.563 23116.683 + 86 K3P+R5 11281.590 95 22753.180 22816.513 23128.491 + 92 K3Pu+F 11872.986 90 23925.973 23981.877 24281.531 + 93 K3Pu+F+I 11611.578 91 23405.157 23462.499 23764.665 + 94 K3Pu+F+G4 11293.905 91 22769.810 22827.153 23129.319 + 95 K3Pu+F+I+G4 11276.791 92 22737.582 22796.386 23101.041 + 96 K3Pu+F+R2 11401.654 92 22987.308 23046.112 23350.767 + 97 K3Pu+F+R3 11280.917 94 22749.834 22811.634 23121.195 + 98 K3Pu+F+R4 11273.862 96 22739.723 22804.615 23118.985 + 99 K3Pu+F+R5 11273.797 98 22743.594 22811.679 23130.757 +105 TPM2+F 11884.006 90 23948.013 24003.917 24303.571 +106 TPM2+F+I 11623.782 91 23429.564 23486.906 23789.072 +107 TPM2+F+G4 11302.139 91 22786.278 22843.620 23145.786 +108 TPM2+F+I+G4 11285.802 92 22755.605 22814.409 23119.064 +109 TPM2+F+R2 11414.326 92 23012.652 23071.456 23376.111 +110 TPM2+F+R3 11289.896 94 22767.792 22829.591 23139.152 +111 TPM2+F+R4 11282.920 96 22757.841 22822.733 23137.102 +112 TPM2+F+R5 11282.887 98 22761.775 22829.859 23148.937 +118 TPM2u+F 11883.999 90 23947.999 24003.903 24303.557 +119 TPM2u+F+I 11623.783 91 23429.565 23486.908 23789.074 +120 TPM2u+F+G4 11302.139 91 22786.278 22843.620 23145.786 +121 TPM2u+F+I+G4 11285.803 92 22755.606 22814.410 23119.065 +122 TPM2u+F+R2 11414.332 92 23012.664 23071.469 23376.123 +123 TPM2u+F+R3 11289.843 94 22767.685 22829.485 23139.046 +124 TPM2u+F+R4 11282.804 96 22757.608 22822.500 23136.870 +125 TPM2u+F+R5 11282.752 98 22761.505 22829.589 23148.668 +131 TPM3+F 11850.105 90 23880.209 23936.114 24235.767 +132 TPM3+F+I 11610.448 91 23402.895 23460.238 23762.404 +133 TPM3+F+G4 11299.536 91 22781.072 22838.414 23140.580 +134 TPM3+F+I+G4 11283.712 92 22751.424 22810.228 23114.883 +135 TPM3+F+R2 11408.626 92 23001.252 23060.056 23364.711 +136 TPM3+F+R3 11286.122 94 22760.244 22822.043 23131.604 +137 TPM3+F+R4 11280.076 96 22752.152 22817.044 23131.414 +138 TPM3+F+R5 11280.042 98 22756.084 22824.168 23143.247 +144 TPM3u+F 11850.106 90 23880.212 23936.116 24235.770 +145 TPM3u+F+I 11610.448 91 23402.895 23460.238 23762.404 +146 TPM3u+F+G4 11299.536 91 22781.073 22838.415 23140.581 +147 TPM3u+F+I+G4 11283.712 92 22751.425 22810.229 23114.884 +148 TPM3u+F+R2 11408.615 92 23001.229 23060.034 23364.689 +149 TPM3u+F+R3 11286.092 94 22760.184 22821.983 23131.544 +150 TPM3u+F+R4 11279.998 96 22751.997 22816.889 23131.259 +151 TPM3u+F+R5 11279.966 98 22755.932 22824.016 23143.095 +157 TIMe 11868.866 88 23913.733 23966.831 24261.390 +158 TIMe+I 11605.100 89 23388.199 23442.689 23739.806 +159 TIMe+G4 11299.969 89 22777.938 22832.428 23129.545 +160 TIMe+I+G4 11281.829 90 22743.658 22799.563 23099.216 +161 TIMe+R2 11405.094 90 22990.188 23046.093 23345.746 +162 TIMe+R3 11283.561 92 22751.122 22809.926 23114.581 +163 TIMe+R4 11277.934 94 22743.868 22805.667 23115.228 +170 TIM+F 11871.107 91 23924.214 23981.557 24283.723 +171 TIM+F+I 11602.595 92 23389.191 23447.995 23752.650 +172 TIM+F+G4 11291.350 92 22766.700 22825.504 23130.159 +173 TIM+F+I+G4 11273.271 93 22732.542 22792.831 23099.951 +174 TIM+F+R2 11399.153 93 22984.307 23044.596 23351.717 +175 TIM+F+R3 11275.789 95 22741.577 22804.911 23116.888 +176 TIM+F+R4 11269.203 97 22732.406 22798.882 23115.619 +177 TIM+F+R5 11269.162 99 22736.323 22806.041 23127.437 +183 TIM2e 11880.064 88 23936.127 23989.226 24283.784 +184 TIM2e+I 11617.349 89 23412.699 23467.189 23764.306 +185 TIM2e+G4 11309.072 89 22796.144 22850.633 23147.751 +186 TIM2e+I+G4 11291.704 90 22763.408 22819.312 23118.966 +187 TIM2e+R2 11418.055 90 23016.111 23072.015 23371.669 +188 TIM2e+R3 11293.443 92 22770.886 22829.691 23134.346 +189 TIM2e+R4 11287.733 94 22763.466 22825.265 23134.826 +196 TIM2+F 11882.064 91 23946.128 24003.470 24305.636 +197 TIM2+F+I 11614.680 92 23413.359 23472.163 23776.818 +198 TIM2+F+G4 11299.528 92 22783.057 22841.861 23146.516 +199 TIM2+F+I+G4 11282.253 93 22750.506 22810.795 23117.915 +200 TIM2+F+R2 11411.683 93 23009.365 23069.655 23376.775 +201 TIM2+F+R3 11284.790 95 22759.580 22822.914 23134.891 +202 TIM2+F+R4 11278.222 97 22750.445 22816.921 23133.657 +203 TIM2+F+R5 11278.190 99 22754.380 22824.099 23145.494 +209 TIM3e 11836.871 88 23849.742 23902.841 24197.399 +210 TIM3e+I 11598.092 89 23374.185 23428.674 23725.792 +211 TIM3e+G4 11302.094 89 22782.188 22836.678 23133.796 +212 TIM3e+I+G4 11285.601 90 22751.202 22807.107 23106.760 +213 TIM3e+R2 11407.386 90 22994.772 23050.677 23350.330 +214 TIM3e+R3 11285.210 92 22754.420 22813.224 23117.879 +215 TIM3e+R4 11281.017 94 22750.034 22811.833 23121.394 +222 TIM3+F 11847.887 91 23877.774 23935.116 24237.282 +223 TIM3+F+I 11601.409 92 23386.818 23445.622 23750.277 +224 TIM3+F+G4 11296.726 92 22777.452 22836.256 23140.911 +225 TIM3+F+I+G4 11279.974 93 22745.948 22806.237 23113.357 +226 TIM3+F+R2 11406.082 93 22998.164 23058.453 23365.573 +227 TIM3+F+R3 11280.913 95 22751.826 22815.159 23127.137 +228 TIM3+F+R4 11275.370 97 22744.740 22811.215 23127.952 +235 TVMe 11826.556 89 23831.113 23885.602 24182.720 +236 TVMe+I 11592.904 90 23365.807 23421.712 23721.365 +237 TVMe+G4 11291.225 90 22762.451 22818.355 23118.009 +238 TVMe+I+G4 11275.287 91 22732.574 22789.917 23092.083 +239 TVMe+R2 11394.816 91 22971.632 23028.974 23331.140 +240 TVMe+R3 11276.244 93 22738.488 22798.777 23105.898 +241 TVMe+R4 11271.891 95 22733.783 22797.116 23109.094 +248 TVM+F 11837.949 92 23859.897 23918.702 24223.357 +249 TVM+F+I 11597.441 93 23380.883 23441.172 23748.293 +250 TVM+F+G4 11286.843 93 22759.686 22819.976 23127.096 +251 TVM+F+I+G4 11270.761 94 22729.521 22791.321 23100.882 +252 TVM+F+R2 11394.360 94 22976.720 23038.520 23348.081 +253 TVM+F+R3 11273.233 96 22738.466 22803.358 23117.728 +254 TVM+F+R4 11267.520 98 22731.039 22799.123 23118.202 +261 SYM 11824.533 90 23829.066 23884.971 24184.624 +262 SYM+I 11584.972 91 23351.944 23409.286 23711.452 +263 SYM+G4 11289.155 91 22760.311 22817.653 23119.819 +264 SYM+I+G4 11272.485 92 22728.970 22787.774 23092.429 +265 SYM+R2 11393.010 92 22970.020 23028.824 23333.479 +266 SYM+R3 11272.191 94 22732.382 22794.181 23103.742 +267 SYM+R4 11268.530 96 22729.060 22793.952 23108.321 +274 GTR+F 11835.789 93 23857.578 23917.868 24224.988 +275 GTR+F+I 11588.515 94 23365.030 23426.829 23736.390 +276 GTR+F+G4 11284.164 94 22756.328 22818.128 23127.689 +277 GTR+F+I+G4 11267.202 95 22724.404 22787.738 23099.715 +278 GTR+F+R2 11392.044 95 22974.088 23037.422 23349.399 +279 GTR+F+R3 11268.292 97 22730.583 22797.059 23113.795 +280 GTR+F+R4 11263.339 99 22724.679 22794.397 23115.792 +Akaike Information Criterion: GTR+F+I+G4 +Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz -CPU time for ModelFinder: 0.073 seconds (0h:0m:0s) -Wall-clock time for ModelFinder: 0.090 seconds (0h:0m:0s) +CPU time for ModelFinder: 0.058 seconds (0h:0m:0s) +Wall-clock time for ModelFinder: 0.062 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, 0.975 / LogL: -11331.956 -Init pinv, alpha: 0.012, 1.000 / Estimate: 0.087, 1.676 / LogL: -11313.524 -Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.677 / LogL: -11313.524 -Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.675 / LogL: -11313.524 -Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.678 / LogL: -11313.523 -Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.674 / LogL: -11313.524 -Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.677 / LogL: -11313.523 -Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.679 / LogL: -11313.521 -Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.682 / LogL: -11313.521 -Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.682 / LogL: -11313.521 -Optimal pinv,alpha: 0.087, 1.682 / LogL: -11313.521 +Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.949 / LogL: -11291.225 +Init pinv, alpha: 0.012, 1.000 / Estimate: 0.084, 1.531 / LogL: -11275.302 +Init pinv, alpha: 0.023, 1.000 / Estimate: 0.084, 1.535 / LogL: -11275.290 +Init pinv, alpha: 0.035, 1.000 / Estimate: 0.084, 1.532 / LogL: -11275.291 +Init pinv, alpha: 0.046, 1.000 / Estimate: 0.084, 1.537 / LogL: -11275.288 +Init pinv, alpha: 0.058, 1.000 / Estimate: 0.084, 1.533 / LogL: -11275.290 +Init pinv, alpha: 0.069, 1.000 / Estimate: 0.085, 1.537 / LogL: -11275.286 +Init pinv, alpha: 0.081, 1.000 / Estimate: 0.085, 1.540 / LogL: -11275.285 +Init pinv, alpha: 0.093, 1.000 / Estimate: 0.085, 1.544 / LogL: -11275.285 +Init pinv, alpha: 0.104, 1.000 / Estimate: 0.085, 1.544 / LogL: -11275.286 +Optimal pinv,alpha: 0.085, 1.540 / LogL: -11275.285 -Parameters optimization took 3.569 sec -Computing ML distances based on estimated model parameters... 0.029 sec +Parameters optimization took 1.912 sec +Computing ML distances based on estimated model parameters... 0.024 sec Computing BIONJ tree... 0.002 seconds -Log-likelihood of BIONJ tree: -11270.546 +Log-likelihood of BIONJ tree: -11271.297 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Generating 98 parsimony trees... 1.211 second -Computing log-likelihood of 98 initial trees ... 6.352 seconds -Current best score: -11237.805 +Generating 98 parsimony trees... 0.750 second +Computing log-likelihood of 98 initial trees ... 2.565 seconds +Current best score: -11237.517 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 1: -11225.551 +BETTER TREE FOUND at iteration 1: -11226.107 Estimate model parameters (epsilon = 0.100) -BETTER TREE FOUND at iteration 2: -11222.776 -Iteration 10 / LogL: -11227.231 / Time: 0h:0m:14s -Iteration 20 / LogL: -11231.953 / Time: 0h:0m:17s -Finish initializing candidate tree set (12) -Current best tree score: -11222.776 / CPU time: 13.726 +BETTER TREE FOUND at iteration 4: -11225.462 +Iteration 10 / LogL: -11232.692 / Time: 0h:0m:7s +BETTER TREE FOUND at iteration 12: -11225.461 +Iteration 20 / LogL: -11225.787 / Time: 0h:0m:9s +Finish initializing candidate tree set (14) +Current best tree score: -11225.461 / CPU time: 7.468 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- -Iteration 30 / LogL: -11252.475 / Time: 0h:0m:20s (0h:0m:50s left) -Iteration 40 / LogL: -11222.781 / Time: 0h:0m:23s (0h:0m:37s left) -Iteration 50 / LogL: -11231.636 / Time: 0h:0m:26s (0h:0m:28s left) -UPDATE BEST LOG-LIKELIHOOD: -11222.775 -Iteration 60 / LogL: -11226.559 / Time: 0h:0m:29s (0h:0m:20s left) -Iteration 70 / LogL: -11234.678 / Time: 0h:0m:32s (0h:0m:14s left) -UPDATE BEST LOG-LIKELIHOOD: -11222.775 -Iteration 80 / LogL: -11223.066 / Time: 0h:0m:35s (0h:0m:9s left) -Iteration 90 / LogL: -11222.791 / Time: 0h:0m:38s (0h:0m:5s left) -Iteration 100 / LogL: -11222.914 / Time: 0h:0m:41s (0h:0m:0s left) -TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:41s +Iteration 30 / LogL: -11233.656 / Time: 0h:0m:12s (0h:0m:36s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 32: -11224.865 +Iteration 40 / LogL: -11228.333 / Time: 0h:0m:16s (0h:0m:38s left) +Iteration 50 / LogL: -11225.106 / Time: 0h:0m:19s (0h:0m:32s left) +Iteration 60 / LogL: -11225.110 / Time: 0h:0m:26s (0h:0m:32s left) +Iteration 70 / LogL: -11226.797 / Time: 0h:0m:44s (0h:0m:40s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 71: -11224.093 +Iteration 80 / LogL: -11225.015 / Time: 0h:0m:53s (0h:1m:2s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 89: -11224.071 +Iteration 90 / LogL: -11225.135 / Time: 0h:1m:18s (0h:1m:27s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 93: -11223.030 +Iteration 100 / LogL: -11224.280 / Time: 0h:1m:45s (0h:1m:39s left) +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 106: -11222.787 +Estimate model parameters (epsilon = 0.100) +BETTER TREE FOUND at iteration 108: -11222.772 +Iteration 110 / LogL: -11222.860 / Time: 0h:2m:6s (0h:1m:53s left) +Iteration 120 / LogL: -11223.344 / Time: 0h:2m:12s (0h:1m:37s left) +Iteration 130 / LogL: -11223.054 / Time: 0h:2m:24s (0h:1m:27s left) +Iteration 140 / LogL: -11224.482 / Time: 0h:2m:29s (0h:1m:12s left) +Iteration 150 / LogL: -11222.868 / Time: 0h:2m:32s (0h:0m:59s left) +Iteration 160 / LogL: -11222.967 / Time: 0h:2m:39s (0h:0m:48s left) +Iteration 170 / LogL: -11222.779 / Time: 0h:2m:48s (0h:0m:37s left) +Iteration 180 / LogL: -11231.545 / Time: 0h:2m:58s (0h:0m:27s left) +Iteration 190 / LogL: -11222.907 / Time: 0h:3m:5s (0h:0m:17s left) +Iteration 200 / LogL: -11227.350 / Time: 0h:3m:19s (0h:0m:8s left) +TREE SEARCH COMPLETED AFTER 209 ITERATIONS / Time: 0h:3m:29s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) -1. Initial log-likelihood: -11222.775 -Optimal log-likelihood: -11222.773 -Rate parameters: A-C: 1.51196 A-G: 2.60325 A-T: 1.66802 C-G: 1.97559 C-T: 2.60325 G-T: 1.00000 +1. Initial log-likelihood: -11222.772 +Optimal log-likelihood: -11222.772 +Rate parameters: A-C: 1.51664 A-G: 2.61142 A-T: 1.67401 C-G: 1.98081 C-T: 2.61142 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 -Proportion of invariable sites: 0.083 -Gamma shape alpha: 1.528 -Parameters optimization took 1 rounds (0.036 sec) -BEST SCORE FOUND : -11222.773 -Total tree length: 12.603 +Proportion of invariable sites: 0.084 +Gamma shape alpha: 1.530 +Parameters optimization took 1 rounds (0.206 sec) +BEST SCORE FOUND : -11222.772 +Total tree length: 12.602 -Total number of iterations: 103 -CPU time used for tree search: 68.012 sec (0h:1m:8s) -Wall-clock time used for tree search: 38.245 sec (0h:0m:38s) -Total CPU time used: 73.834 sec (0h:1m:13s) -Total wall-clock time used: 41.971 sec (0h:0m:41s) +Total number of iterations: 209 +CPU time used for tree search: 218.043 sec (0h:3m:38s) +Wall-clock time used for tree search: 207.812 sec (0h:3m:27s) +Total CPU time used: 222.205 sec (0h:3m:42s) +Total wall-clock time used: 210.029 sec (0h:3m:30s) Analysis results written to: IQ-TREE report: example.phy.iqtree @@ -5379,12 +5429,14 @@ Likelihood distances: example.phy.mldist Screen log file: example.phy.log -Date and Time: Mon Jan 30 07:22:51 2023 -73.93user 0.70system 0:42.08elapsed 177%CPU (0avgtext+0avgdata 12256maxresident)k -0inputs+0outputs (0major+1309minor)pagefaults 0swaps -+ rm -rf /tmp/iqtree-test.P8nuZ7 -222.40user 1.84system 3:45.41elapsed 99%CPU (0avgtext+0avgdata 14480maxresident)k -0inputs+0outputs (0major+7457minor)pagefaults 0swaps +Date and Time: Wed Dec 29 03:13:45 2021 + +real 3m30.133s +user 3m42.298s +sys 0m1.893s ++ rm -rf /tmp/iqtree-test.km5V14 +321.68user 2.50system 5:10.21elapsed 104%CPU (0avgtext+0avgdata 15020maxresident)k +0inputs+0outputs (0major+6358minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-1.6.12+dfsg' create-stamp debian/debhelper-build-stamp @@ -5395,7 +5447,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-1.6.12+dfsg' dh_auto_install -Bbuild.omp - cd build.omp && make -j16 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.omp && make -j15 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.12+dfsg/build.omp//CMakeFiles/progress.marks @@ -5408,26 +5460,26 @@ make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/gsl /build/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/ncl /build/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb /build/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.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-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/nclextra /build/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= @@ -5440,38 +5492,38 @@ make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.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-1.6.12+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. +make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 2%] Built target lbfgsb +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 3%] Built target vectorclass make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 3%] Built target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 7%] Built target gsl -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 8%] Built target pllavx [ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' @@ -5493,11 +5545,13 @@ [ 15%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend [ 25%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/pda /build/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/alignment /build/iqtree-1.6.12+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' @@ -5507,37 +5561,35 @@ make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +[ 41%] Built target pll +[ 42%] Built target kernelfma +[ 43%] Built target kernelavx make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build +[ 44%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 41%] Built target pll -[ 42%] Built target kernelavx -[ 43%] Built target kernelfma -[ 44%] Built target kernelsse -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +[ 52%] Built target whtest +[ 55%] Built target utils +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 50%] Built target whtest +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' +cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/model /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/model /build/iqtree-1.6.12+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' -[ 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-1.6.12+dfsg/build.omp' -cd /build/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/model /build/iqtree-1.6.12+dfsg/build.omp /build/iqtree-1.6.12+dfsg/build.omp/model /build/iqtree-1.6.12+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= [ 68%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build @@ -5582,7 +5634,7 @@ -- Installing: /build/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.omp' dh_auto_install -Bbuild.serial - cd build.serial && make -j16 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.serial && make -j15 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.12+dfsg/build.serial//CMakeFiles/progress.marks @@ -5596,78 +5648,78 @@ make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/gsl /build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.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 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-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/gsl /build/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/ncl /build/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb /build/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/nclextra /build/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/vectorclass /build/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/sprng /build/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build +[ 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-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 2%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 3%] Built target vectorclass -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +[ 4%] Built target pllavx +[ 8%] Built target gsl make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -[ 7%] Built target gsl -[ 8%] Built target pllavx +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build [ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build @@ -5677,46 +5729,46 @@ make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -[ 15%] Built target nclextra +[ 22%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +[ 25%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend -[ 25%] Built target ncl make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/alignment /build/iqtree-1.6.12+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pda /build/iqtree-1.6.12+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' +make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. +make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/pda /build/iqtree-1.6.12+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +[ 41%] Built target pll +[ 42%] Built target kernelavx +[ 43%] Built target kernelfma +[ 44%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' -cd /build/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.serial /build/iqtree-1.6.12+dfsg/build.serial/alignment /build/iqtree-1.6.12+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= -[ 26%] Built target kernelfma -[ 36%] Built target kernelavx -[ 37%] Built target kernelsse -[ 50%] Built target pll -[ 50%] Built target whtest -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +[ 50%] Built target whtest +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' @@ -5767,7 +5819,7 @@ -- Up-to-date: /build/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.serial' dh_auto_install -Bbuild.mpi - cd build.mpi && make -j16 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build.mpi && make -j15 install DESTDIR=/build/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.12+dfsg -B/build/iqtree-1.6.12+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.12+dfsg/build.mpi//CMakeFiles/progress.marks @@ -5781,136 +5833,136 @@ make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/gsl /build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.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 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-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/gsl /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/gsl /build/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/ncl /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/ncl /build/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pll /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/sprng /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/sprng /build/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass /build/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/nclextra /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/whtest /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/whtest /build/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 2%] Built target lbfgsb +make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= +[ 3%] Built target vectorclass make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build -[ 1%] Built target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build -[ 5%] Built target gsl make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build -[ 7%] Built target lbfgsb -make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/utils /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= -[ 11%] Built target sprng +make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build +make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build +make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build +[ 7%] Built target gsl +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build +[ 11%] Built target sprng make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build -[ 14%] Built target nclextra -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= -[ 15%] Built target pllavx -[ 25%] Built target ncl -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend -make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/alignment /build/iqtree-1.6.12+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 12%] Built target pllavx +[ 15%] Built target nclextra +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend +[ 25%] Built target ncl +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend +[ 26%] Built target kernelavx make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 26%] Built target kernelfma -[ 27%] Built target kernelsse -[ 28%] Built target kernelavx +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/pda /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= +[ 27%] Built target kernelfma +[ 28%] Built target kernelsse +make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' +cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/alignment /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/alignment /build/iqtree-1.6.12+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 44%] Built target pll -make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 44%] Built target pll [ 50%] Built target whtest make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. +make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 59%] Built target pda +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build +make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' -make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. +make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' +[ 55%] Built target utils +make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' -[ 64%] Built target utils -make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend -[ 68%] Built target alignment make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.12+dfsg /build/iqtree-1.6.12+dfsg/model /build/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-1.6.12+dfsg/build.mpi/model /build/iqtree-1.6.12+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= +[ 64%] Built target pda +[ 68%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.12+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.12+dfsg/build.mpi' @@ -5997,8 +6049,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'iqtree' in '../iqtree_1.6.12+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_1.6.12+dfsg-1_amd64.deb'. +dpkg-deb: building package 'iqtree' in '../iqtree_1.6.12+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iqtree_1.6.12+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -6006,12 +6058,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/1732826/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1732826/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/270558 and its subdirectories -I: Current time: Mon Jan 30 07:25:12 -12 2023 -I: pbuilder-time-stamp: 1675106712 +I: removing directory /srv/workspace/pbuilder/1732826 and its subdirectories +I: Current time: Wed Dec 29 03:16:15 +14 2021 +I: pbuilder-time-stamp: 1640697375