I: pbuilder: network access will be disabled during build I: Current time: Sun Jul 4 03:23:07 +14 2021 I: pbuilder-time-stamp: 1625318587 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [iqtree_1.6.9+dfsg-1.dsc] I: copying [./iqtree_1.6.9+dfsg.orig.tar.xz] I: copying [./iqtree_1.6.9+dfsg-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Thu Jan 3 03:51:35 2019 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./iqtree_1.6.9+dfsg-1.dsc dpkg-source: info: extracting iqtree in iqtree-1.6.9+dfsg dpkg-source: info: unpacking iqtree_1.6.9+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_1.6.9+dfsg-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/42517/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/42517/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/42517/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0f4cf3b358324b1399f4568b922e5e04 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=42517 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/pbuilderrc_wFQ8 --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.tWVBNBrTnZ/b2 --logfile b2/build.log iqtree_1.6.9+dfsg-1.dsc' SUDO_GID=111 SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-2 (2021-06-21) x86_64 GNU/Linux I: ls -l /bin total 5116 -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash -rwxr-xr-x 1 root root 109408 Mar 1 2019 date -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd -rwxr-xr-x 1 root root 93744 Mar 1 2019 df -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 35424 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln -rwxr-xr-x 1 root root 56760 Jul 27 2018 login -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 43008 Jan 10 2019 more -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 4 03:23 sh -> bash lrwxrwxrwx 1 root root 4 Jun 21 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty -rwsr-xr-x 1 root root 63568 Jan 10 2019 su -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch -rwxr-xr-x 1 root root 35424 Mar 1 2019 true -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/42517/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), cmake, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libsprng2-dev; however: Package libsprng2-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on time; however: Package time is not installed. pbuilder-satisfydepends-dummy depends on chrpath; however: Package chrpath is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} chrpath{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libbsd0{a} libcroco3{a} libcurl4{a} libedit2{a} libeigen3-dev{a} libelf1{a} libevent-2.1-6{a} libevent-core-2.1-6{a} libevent-pthreads-2.1-6{a} libexpat1{a} libfabric1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libgmp-dev{a} libgmpxx4ldbl{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc5{a} libibverbs-dev{a} libibverbs1{a} libicu63{a} libjsoncpp1{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.4-2{a} libldap-common{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libncurses6{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpipeline1{a} libpmix2{a} libprocps7{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libsprng2{a} libsprng2-dev{a} libssh2-1{a} libssl1.1{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} lsb-base{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} po-debconf{a} procps{a} sensible-utils{a} time{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libgpm2 libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 101 newly installed, 0 to remove and 0 not upgraded. Need to get 39.4 MB of archives. After unpacking 152 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get: 2 http://deb.debian.org/debian buster/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get: 3 http://deb.debian.org/debian buster/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get: 4 http://deb.debian.org/debian buster/main amd64 groff-base amd64 1.22.4-3+deb10u1 [916 kB] Get: 5 http://deb.debian.org/debian buster/main amd64 libpipeline1 amd64 1.5.1-2 [31.2 kB] Get: 6 http://deb.debian.org/debian buster/main amd64 man-db amd64 2.8.5-2 [1274 kB] Get: 7 http://deb.debian.org/debian buster/main amd64 liblocale-gettext-perl amd64 1.07-3+b4 [18.9 kB] Get: 8 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get: 9 http://deb.debian.org/debian buster/main amd64 libprocps7 amd64 2:3.3.15-2 [61.7 kB] Get: 10 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get: 11 http://deb.debian.org/debian buster/main amd64 procps amd64 2:3.3.15-2 [259 kB] Get: 12 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get: 13 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get: 14 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get: 15 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get: 16 http://deb.debian.org/debian buster/main amd64 gettext-base amd64 0.19.8.1-9 [123 kB] Get: 17 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get: 18 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get: 19 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u1 [65.8 kB] Get: 20 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u1 [122 kB] Get: 21 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u6 [1539 kB] Get: 22 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u1 [369 kB] Get: 23 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u1 [158 kB] Get: 24 http://deb.debian.org/debian buster/main amd64 openssh-client amd64 1:7.9p1-10+deb10u2 [782 kB] Get: 25 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get: 26 http://deb.debian.org/debian buster/main amd64 m4 amd64 1.4.18-2 [203 kB] Get: 27 http://deb.debian.org/debian buster/main amd64 autoconf all 2.69-11 [341 kB] Get: 28 http://deb.debian.org/debian buster/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get: 29 http://deb.debian.org/debian buster/main amd64 automake all 1:1.16.1-4 [771 kB] Get: 30 http://deb.debian.org/debian buster/main amd64 autopoint all 0.19.8.1-9 [434 kB] Get: 31 http://deb.debian.org/debian buster/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 32 http://deb.debian.org/debian buster/main amd64 cmake-data all 3.13.4-1 [1476 kB] Get: 33 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u1 [8300 kB] Get: 34 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u2 [689 kB] Get: 35 http://deb.debian.org/debian buster/main amd64 libarchive13 amd64 3.3.3-4+deb10u1 [313 kB] Get: 36 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get: 37 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get: 38 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get: 39 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get: 40 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get: 41 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get: 42 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get: 43 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get: 44 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get: 45 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get: 46 http://deb.debian.org/debian buster/main amd64 libjsoncpp1 amd64 1.7.4-3 [75.6 kB] Get: 47 http://deb.debian.org/debian buster/main amd64 librhash0 amd64 1.3.8-1 [122 kB] Get: 48 http://deb.debian.org/debian buster/main amd64 libuv1 amd64 1.24.1-1 [110 kB] Get: 49 http://deb.debian.org/debian buster/main amd64 cmake amd64 3.13.4-1 [3480 kB] Get: 50 http://deb.debian.org/debian buster/main amd64 libtool all 2.4.6-9 [547 kB] Get: 51 http://deb.debian.org/debian buster/main amd64 dh-autoreconf all 19 [16.9 kB] Get: 52 http://deb.debian.org/debian buster/main amd64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 53 http://deb.debian.org/debian buster/main amd64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 54 http://deb.debian.org/debian buster/main amd64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 55 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get: 56 http://deb.debian.org/debian buster/main amd64 dwz amd64 0.12-3 [78.0 kB] Get: 57 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get: 58 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get: 59 http://deb.debian.org/debian buster/main amd64 gettext amd64 0.19.8.1-9 [1303 kB] Get: 60 http://deb.debian.org/debian buster/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 61 http://deb.debian.org/debian buster/main amd64 po-debconf all 1.0.21 [248 kB] Get: 62 http://deb.debian.org/debian buster/main amd64 debhelper all 12.1.1 [1016 kB] Get: 63 http://deb.debian.org/debian buster/main amd64 help2man amd64 1.47.8 [177 kB] Get: 64 http://deb.debian.org/debian buster/main amd64 libnl-3-200 amd64 3.4.0-1 [63.0 kB] Get: 65 http://deb.debian.org/debian buster/main amd64 libnl-route-3-200 amd64 3.4.0-1 [162 kB] Get: 66 http://deb.debian.org/debian buster/main amd64 libibverbs1 amd64 22.1-1 [51.2 kB] Get: 67 http://deb.debian.org/debian buster/main amd64 ibverbs-providers amd64 22.1-1 [187 kB] Get: 68 http://deb.debian.org/debian buster/main amd64 pkg-config amd64 0.29-6 [63.5 kB] Get: 69 http://deb.debian.org/debian buster/main amd64 libeigen3-dev all 3.3.7-1 [850 kB] Get: 70 http://deb.debian.org/debian buster/main amd64 libevent-2.1-6 amd64 2.1.8-stable-4 [177 kB] Get: 71 http://deb.debian.org/debian buster/main amd64 libevent-core-2.1-6 amd64 2.1.8-stable-4 [129 kB] Get: 72 http://deb.debian.org/debian buster/main amd64 libevent-pthreads-2.1-6 amd64 2.1.8-stable-4 [47.9 kB] Get: 73 http://deb.debian.org/debian buster/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6 [168 kB] Get: 74 http://deb.debian.org/debian buster/main amd64 libnuma1 amd64 2.0.12-1 [26.2 kB] Get: 75 http://deb.debian.org/debian buster/main amd64 libpsm2-2 amd64 11.2.78-1 [177 kB] Get: 76 http://deb.debian.org/debian buster/main amd64 librdmacm1 amd64 22.1-1 [65.3 kB] Get: 77 http://deb.debian.org/debian buster/main amd64 libfabric1 amd64 1.6.2-3 [396 kB] Get: 78 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get: 79 http://deb.debian.org/debian buster/main amd64 libgmpxx4ldbl amd64 2:6.1.2+dfsg-4 [22.9 kB] Get: 80 http://deb.debian.org/debian buster/main amd64 libgmp-dev amd64 2:6.1.2+dfsg-4 [628 kB] Get: 81 http://deb.debian.org/debian buster/main amd64 libltdl7 amd64 2.4.6-9 [390 kB] Get: 82 http://deb.debian.org/debian buster/main amd64 libhwloc5 amd64 1.11.12-3 [111 kB] Get: 83 http://deb.debian.org/debian buster/main amd64 libnuma-dev amd64 2.0.12-1 [39.2 kB] Get: 84 http://deb.debian.org/debian buster/main amd64 libltdl-dev amd64 2.4.6-9 [162 kB] Get: 85 http://deb.debian.org/debian buster/main amd64 libhwloc-dev amd64 1.11.12-3 [175 kB] Get: 86 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get: 87 http://deb.debian.org/debian buster/main amd64 ocl-icd-libopencl1 amd64 2.2.12-2 [37.5 kB] Get: 88 http://deb.debian.org/debian buster/main amd64 libhwloc-plugins amd64 1.11.12-3 [17.4 kB] Get: 89 http://deb.debian.org/debian buster/main amd64 libnl-3-dev amd64 3.4.0-1 [102 kB] Get: 90 http://deb.debian.org/debian buster/main amd64 libnl-route-3-dev amd64 3.4.0-1 [177 kB] Get: 91 http://deb.debian.org/debian buster/main amd64 libibverbs-dev amd64 22.1-1 [362 kB] Get: 92 http://deb.debian.org/debian buster/main amd64 libpmix2 amd64 3.1.2-3 [498 kB] Get: 93 http://deb.debian.org/debian buster/main amd64 libopenmpi3 amd64 3.1.3-11 [2191 kB] Get: 94 http://deb.debian.org/debian buster/main amd64 openmpi-common all 3.1.3-11 [165 kB] Get: 95 http://deb.debian.org/debian buster/main amd64 openmpi-bin amd64 3.1.3-11 [200 kB] Get: 96 http://deb.debian.org/debian buster/main amd64 libopenmpi-dev amd64 3.1.3-11 [974 kB] Get: 97 http://deb.debian.org/debian buster/main amd64 libsprng2 amd64 2.0a-12 [75.7 kB] Get: 98 http://deb.debian.org/debian buster/main amd64 libsprng2-dev amd64 2.0a-12 [79.2 kB] Get: 99 http://deb.debian.org/debian buster/main amd64 mpi-default-dev amd64 1.13 [5476 B] Get: 100 http://deb.debian.org/debian buster/main amd64 time amd64 1.7-25.1+b1 [31.6 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-1 [214 kB] Fetched 39.4 MB in 1s (27.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.9.1-2+deb10u1_amd64.deb ... Unpacking libbsd0:amd64 (0.9.1-2+deb10u1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Unpacking libk5crypto3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../020-libssl1.1_1.1.1d-0+deb10u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1d-0+deb10u6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../021-libkrb5-3_1.17-3+deb10u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../022-libgssapi-krb5-2_1.17-3+deb10u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.17-3+deb10u1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../023-openssh-client_1%3a7.9p1-10+deb10u2_amd64.deb ... Unpacking openssh-client (1:7.9p1-10+deb10u2) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../024-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. 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Preparing to unpack .../037-libldap-common_2.4.47+dfsg-3+deb10u6_all.deb ... Unpacking libldap-common (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../038-libldap-2.4-2_2.4.47+dfsg-3+deb10u6_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../039-libnghttp2-14_1.36.0-2+deb10u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../040-libpsl5_0.20.2-2_amd64.deb ... Unpacking libpsl5:amd64 (0.20.2-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../041-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../042-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../043-libcurl4_7.64.0-4+deb10u2_amd64.deb ... Unpacking libcurl4:amd64 (7.64.0-4+deb10u2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../044-libexpat1_2.2.6-2+deb10u1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.6-2+deb10u1) ... Selecting previously unselected package libjsoncpp1:amd64. Preparing to unpack .../045-libjsoncpp1_1.7.4-3_amd64.deb ... Unpacking libjsoncpp1:amd64 (1.7.4-3) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../046-librhash0_1.3.8-1_amd64.deb ... Unpacking librhash0:amd64 (1.3.8-1) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../047-libuv1_1.24.1-1_amd64.deb ... Unpacking libuv1:amd64 (1.24.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../048-cmake_3.13.4-1_amd64.deb ... Unpacking cmake (3.13.4-1) ... Selecting previously unselected package libtool. Preparing to unpack .../049-libtool_2.4.6-9_all.deb ... Unpacking libtool (2.4.6-9) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../050-dh-autoreconf_19_all.deb ... Unpacking dh-autoreconf (19) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../051-libarchive-zip-perl_1.64-1_all.deb ... Unpacking libarchive-zip-perl (1.64-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../052-libfile-stripnondeterminism-perl_1.1.2-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.1.2-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../053-dh-strip-nondeterminism_1.1.2-1_all.deb ... Unpacking dh-strip-nondeterminism (1.1.2-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../054-libelf1_0.176-1.1_amd64.deb ... Unpacking libelf1:amd64 (0.176-1.1) ... Selecting previously unselected package dwz. Preparing to unpack .../055-dwz_0.12-3_amd64.deb ... Unpacking dwz (0.12-3) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../056-libglib2.0-0_2.58.3-2+deb10u3_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Selecting previously unselected package libcroco3:amd64. Preparing to unpack .../057-libcroco3_0.6.12-3_amd64.deb ... Unpacking libcroco3:amd64 (0.6.12-3) ... Selecting previously unselected package gettext. Preparing to unpack .../058-gettext_0.19.8.1-9_amd64.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../059-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../060-po-debconf_1.0.21_all.deb ... Unpacking po-debconf (1.0.21) ... 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Selecting previously unselected package pkg-config. Preparing to unpack .../067-pkg-config_0.29-6_amd64.deb ... Unpacking pkg-config (0.29-6) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../068-libeigen3-dev_3.3.7-1_all.deb ... Unpacking libeigen3-dev (3.3.7-1) ... Selecting previously unselected package libevent-2.1-6:amd64. Preparing to unpack .../069-libevent-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-core-2.1-6:amd64. Preparing to unpack .../070-libevent-core-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-core-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libevent-pthreads-2.1-6:amd64. Preparing to unpack .../071-libevent-pthreads-2.1-6_2.1.8-stable-4_amd64.deb ... Unpacking libevent-pthreads-2.1-6:amd64 (2.1.8-stable-4) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../072-libpsm-infinipath1_3.3+20.604758e7-6_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../073-libnuma1_2.0.12-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.12-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../074-libpsm2-2_11.2.78-1_amd64.deb ... Unpacking libpsm2-2 (11.2.78-1) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../075-librdmacm1_22.1-1_amd64.deb ... Unpacking librdmacm1:amd64 (22.1-1) ... Selecting previously unselected package libfabric1. Preparing to unpack .../076-libfabric1_1.6.2-3_amd64.deb ... Unpacking libfabric1 (1.6.2-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../077-libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... Selecting previously unselected package libgmpxx4ldbl:amd64. 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Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/iqtree-1.6.9+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 1.6.9+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-1.6.9+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/gsl /build/iqtree-1.6.9+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/ncl /build/iqtree-1.6.9+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pll /build/iqtree-1.6.9+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/nclextra /build/iqtree-1.6.9+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/whtest /build/iqtree-1.6.9+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/sprng /build/iqtree-1.6.9+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/vectorclass /build/iqtree-1.6.9+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target kernelavx Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target pll make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build Scanning dependencies of target ncl Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build Scanning dependencies of target kernelsse [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 2%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o [ 3%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp [ 4%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp [ 5%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp [ 7%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o [ 8%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c [ 9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp [ 9%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 10%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c [ 11%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 11%] Linking CXX static library libvectorclass.a [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 12%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 14%] Built target vectorclass [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c [ 16%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp [ 17%] Linking CXX static library libgsl.a cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 18%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c cd /build/iqtree-1.6.9+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c [ 18%] Built target gsl [ 19%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp [ 20%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c [ 21%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake [ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c cd /build/iqtree-1.6.9+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 21%] Built target sprng [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ [ 24%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp [ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 25%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c [ 26%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp [ 28%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c [ 28%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c [ 29%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c [ 31%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ [ 31%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 33%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 33%] Built target pllavx [ 33%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp [ 34%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 34%] Built target lbfgsb [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/utils /build/iqtree-1.6.9+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 35%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 36%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp [ 36%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp [ 36%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp [ 39%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 40%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a [ 41%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp [ 41%] Built target whtest [ 41%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp [ 42%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 43%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp [ 44%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 44%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c [ 45%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c [ 46%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 46%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 47%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp [ 47%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o [ 48%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 49%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c [ 49%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c [ 50%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 50%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c [ 51%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 51%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 52%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c [ 53%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 53%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 53%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp [ 58%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 58%] Built target pll [ 59%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /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-1.6.9+dfsg/build.omp' [ 59%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pda /build/iqtree-1.6.9+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 59%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c [ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 67%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp [ 76%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 76%] Built target pda [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 84%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target alignment [ 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 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target kernelsse [ 84%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 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-1.6.9+dfsg/build.omp' [ 84%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/tree /build/iqtree-1.6.9+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' # 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 -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend Scanning dependencies of target gsl Scanning dependencies of target ncl make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target nclextra make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target vectorclass make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build Scanning dependencies of target sprng Scanning dependencies of target pll [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp Scanning dependencies of target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Scanning dependencies of target kernelsse make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 3%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp [ 5%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp [ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp [ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o [ 7%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c [ 9%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c [ 10%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp [ 11%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp [ 11%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp [ 14%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 15%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 16%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c [ 16%] Linking CXX static library libgsl.a cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 16%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c cd /build/iqtree-1.6.9+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp [ 16%] Built target vectorclass /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp [ 17%] Built target gsl [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o [ 18%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c [ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 19%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 19%] Built target sprng [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 21%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp [ 23%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c [ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp [ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c [ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp [ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c [ 27%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ [ 28%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp [ 29%] Built target pllavx [ 30%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp [ 31%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 31%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 32%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 33%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ [ 34%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp [ 35%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c [ 36%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp [ 37%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp [ 37%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 38%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp [ 39%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 39%] Built target whtest [ 39%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 40%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 41%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c [ 41%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 42%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ [ 43%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 43%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 43%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp [ 44%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp [ 45%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 46%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o [ 46%] Building C object pll/CMakeFiles/pll.dir/queue.c.o /usr/bin/ranlib libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 46%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 47%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c [ 47%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 48%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 48%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 49%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 50%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 51%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 51%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c [ 52%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c [ 52%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp [ 54%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c [ 54%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c [ 55%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 56%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ /usr/bin/ranlib libncl.a In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 57%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= [ 57%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp [ 61%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 61%] Built target pll [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c [ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp [ 68%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/model /build/iqtree-1.6.9+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 77%] Built target pda [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 84%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target alignment [ 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 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target kernelsse [ 84%] Linking CXX static library 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-1.6.9+dfsg/build.serial' [ 84%] Built target kernelavx [ 84%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target kernelfma [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/tree /build/iqtree-1.6.9+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/build/iqtree-1.6.9+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' # 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 -j15 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/mympi.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/gsl /build/iqtree-1.6.9+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/ncl /build/iqtree-1.6.9+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build Scanning dependencies of target mympi make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend Scanning dependencies of target gsl make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target lbfgsb Scanning dependencies of target kernelsse [ 0%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build [ 0%] Building CXX object CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o Scanning dependencies of target nclextra make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build Scanning dependencies of target pllavx Scanning dependencies of target vectorclass /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/TreeCollection.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 0%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target sprng make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Scanning dependencies of target whtest Scanning dependencies of target ncl [ 1%] Building CXX object CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/ObjectStream.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/multinomial.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build [ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/binomial_tpe.cpp make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-1.6.9+dfsg/lbfgsb/lbfgsb_new.cpp [ 4%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o [ 5%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylokernelsse.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o [ 7%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsassumptionsblock.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-1.6.9+dfsg/vectorclass/instrset_detect.cpp Scanning dependencies of target pll [ 8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/mpdablock.cpp make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 9%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o [ 10%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen.c cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/lcg64.c [ 10%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-1.6.9+dfsg/pll/alignment.c In file included from /build/iqtree-1.6.9+dfsg/pll/alignment.c:40: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/pow_int.cpp [ 11%] Linking CXX static library libvectorclass.a cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 11%] Built target vectorclass [ 11%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-1.6.9+dfsg/sprng/makeseed.c [ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o [ 12%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gauss.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-1.6.9+dfsg/sprng/memory.c [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gaussinv.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c In file included from /build/iqtree-1.6.9+dfsg/pll/avxLikelihood.c:57: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 15%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-1.6.9+dfsg/sprng/store.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-1.6.9+dfsg/sprng/primes-lcg64.c [ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-1.6.9+dfsg/gsl/gausspdf.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:29: /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); ^~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-1.6.9+dfsg/sprng/checkid.c [ 18%] Linking CXX static library libgsl.a [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsblock.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c cd /build/iqtree-1.6.9+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 19%] Linking C static library libsprng.a cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake [ 19%] Built target gsl In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); ^~~~~~~~~~~~~~~~~~ [ 20%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-1.6.9+dfsg/whtest/eigen_sym.c /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 20%] Built target sprng [ 20%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-1.6.9+dfsg/whtest/random.c [ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda.c [ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/weisslambda_sub.c [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest.c [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxscharactersblock.cpp [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c [ 23%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/whtest/whtest_wrapper.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdatablock.cpp /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf ( ifp, "%c", &c ); ^~~~~~~~~~~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c [ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msetsblock.cpp [ 25%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-1.6.9+dfsg/pll/hardware.c In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-1.6.9+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf (fd, "%d", &id); ^~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-1.6.9+dfsg/pll/hash.c [ 26%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-1.6.9+dfsg/pll/lexer.c [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretedatum.cpp [ 27%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdiscretematrix.cpp [ 28%] Linking C static library libpllavx.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 In file included from /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 28%] Built target pllavx [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancedatum.cpp [ 28%] Linking CXX static library liblbfgsb.a cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 28%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 29%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/eigendecomposition.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-1.6.9+dfsg/pll/models.c [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/models.c:53: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsemptyblock.cpp [ 31%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-1.6.9+dfsg/pll/newick.c In file included from /build/iqtree-1.6.9+dfsg/pll/newick.c:36: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 32%] Linking CXX static library libwhtest.a cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 32%] Built target whtest [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsexception.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsreader.cpp [ 35%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c [ 36%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/msplitsblock.cpp [ 36%] Linking CXX static library libmympi.a /usr/bin/cmake -P CMakeFiles/mympi.dir/cmake_clean_target.cmake In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); ^~~~~~~~~~~~~~~~~~ /usr/bin/cmake -E cmake_link_script CMakeFiles/mympi.dir/link.txt --verbose=1 [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxssetreader.cpp /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); ^~~~~~~~~~~~~~~~~~ /usr/bin/ar qc libmympi.a CMakeFiles/mympi.dir/utils/TreeCollection.cpp.o CMakeFiles/mympi.dir/utils/ObjectStream.cpp.o /usr/bin/ranlib libmympi.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 36%] Built target mympi [ 36%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/genericParallelization.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstaxablock.cpp [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstoken.cpp [ 39%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c In file included from /build/iqtree-1.6.9+dfsg/pll/optimizeModel.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 39%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/gzstream.cpp [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-1.6.9+dfsg/ncl/nxstreesblock.cpp [ 40%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/optimization.cpp [ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-1.6.9+dfsg/nclextra/modelsblock.cpp [ 41%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/stoprule.cpp [ 41%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/tools.cpp [ 41%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-1.6.9+dfsg/pll/parsePartition.c In file included from /build/iqtree-1.6.9+dfsg/pll/parsePartition.c:42: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 42%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/pllnni.cpp [ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-1.6.9+dfsg/pll/queue.c [ 43%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-1.6.9+dfsg/pll/randomTree.c [ 44%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-1.6.9+dfsg/pll/recom.c [ 45%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c In file included from /build/iqtree-1.6.9+dfsg/pll/randomTree.c:37: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 45%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/checkpoint.cpp In file included from /build/iqtree-1.6.9+dfsg/pll/recom.c:43: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o In file included from /build/iqtree-1.6.9+dfsg/pll/restartHashTable.c:47: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c [ 46%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-1.6.9+dfsg/pll/ssort.c In file included from /build/iqtree-1.6.9+dfsg/pll/searchAlgo.c:51: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-1.6.9+dfsg/pll/stack.c [ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-1.6.9+dfsg/pll/topologies.c In file included from /build/iqtree-1.6.9+dfsg/pll/topologies.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 47%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-1.6.9+dfsg/pll/trash.c In file included from /build/iqtree-1.6.9+dfsg/pll/trash.c:48: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ [ 48%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-1.6.9+dfsg/pll/treeIO.c [ 49%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-1.6.9+dfsg/pll/utils.c In file included from /build/iqtree-1.6.9+dfsg/pll/treeIO.c:49: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/pll/pllInternal.h:16, from /build/iqtree-1.6.9+dfsg/pll/utils.c:70: /build/iqtree-1.6.9+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); ^~~~~~~~~~~~~~~~~~ /build/iqtree-1.6.9+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign', declared with attribute warn_unused_result [-Wunused-result] #define rax_posix_memalign posix_memalign /build/iqtree-1.6.9+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * ^~~~~~~~~~~~~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-1.6.9+dfsg/utils/MPIHelper.cpp [ 51%] Linking CXX static library libnclextra.a cd /build/iqtree-1.6.9+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+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-1.6.9+dfsg/build.mpi' [ 51%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o [ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/circularnetwork.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/greedy.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/gurobiwrapper.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/hashsplitset.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdnetwork.cpp [ 54%] Linking C static library libpll.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 54%] Built target pll [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pruning.cpp [ 55%] Linking CXX static library libncl.a cd /build/iqtree-1.6.9+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+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-1.6.9+dfsg/build.mpi' [ 55%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/alignment /build/iqtree-1.6.9+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/pattern.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/split.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitgraph.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/splitset.cpp [ 57%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-1.6.9+dfsg/pda/lpwrapper.c [ 58%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopd.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/graph.cpp [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtree.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/pdtreeset.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/pda/ecopdmtreeset.cpp [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/alignmentpairwise.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/maalignment.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignment.cpp /build/iqtree-1.6.9+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwise.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-1.6.9+dfsg/alignment/superalignmentpairwiseplen.cpp [ 63%] Linking CXX static library libutils.a cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/model /build/iqtree-1.6.9+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelbin.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modeldna.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelset.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodel.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelsubst.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:20: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelset.h:23, from /build/iqtree-1.6.9+dfsg/model/modelset.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.h:23, from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelbin.h:23, from /build/iqtree-1.6.9+dfsg/model/modelbin.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:24: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:26: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:27: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactory.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ [ 69%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategamma.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rategammainvar.cpp [ 71%] Linking CXX static library libpda.a cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 71%] Built target pda [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateinvar.cpp /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerdiscrete.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratemeyerhaeseler.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratekategory.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefree.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/ratefreeinvar.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachy.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-1.6.9+dfsg/model/rateheterotachyinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/model/ratefree.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelcodon.h:11, from /build/iqtree-1.6.9+dfsg/model/modelcodon.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:11, from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:10: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.cpp:13: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelunrest.h:11, from /build/iqtree-1.6.9+dfsg/model/modelunrest.cpp:8: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.h:14, from /build/iqtree-1.6.9+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modeldna.h:23, from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelpomo.h:4, from /build/iqtree-1.6.9+dfsg/model/modelpomo.cpp:1: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.h:11, from /build/iqtree-1.6.9+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 81%] Linking CXX static library libalignment.a cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 81%] Built target alignment [ 81%] 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 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 81%] Built target kernelsse [ 82%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 82%] Built target kernelfma [ 83%] 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-1.6.9+dfsg/build.mpi' [ 83%] Built target kernelavx [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/tree /build/iqtree-1.6.9+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/constrainttree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/matree.cpp [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/candidateset.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/memslot.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mexttree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/ncbitree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/mtree.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonode.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/node.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylosupertreeplen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp In file included from /build/iqtree-1.6.9+dfsg/tree/iqtree.cpp:29: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:34: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/tinatree.cpp In file included from /build/iqtree-1.6.9+dfsg/model/modelmixture.h:13, from /build/iqtree-1.6.9+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-1.6.9+dfsg/tree/parstree.cpp /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-1.6.9+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [ 97%] Linking CXX static library libtree.a cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-1.6.9+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-1.6.9+dfsg/main/main.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-1.6.9+dfsg/obsolete/parsmultistate.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-1.6.9+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-1.6.9+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp /build/iqtree-1.6.9+dfsg/main/main.cpp:235:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; ^~~~~~~~ /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl ^~~~~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:20: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:21: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:30: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:33: /build/iqtree-1.6.9+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /build/iqtree-1.6.9+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-1.6.9+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /build/iqtree-1.6.9+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-1.6.9+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /build/iqtree-1.6.9+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ [100%] Linking CXX executable iqtree-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree-mpi -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a libmympi.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' # 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 override_dh_auto_build make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo' >> example.short time sh example.short Executing tests using /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp ... + /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy Seed: 652437 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sun Jul 4 03:38:31 2021 Kernel: AVX - 1 threads (15 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 15 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.016 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 JC 12015.193 85 24200.386 24249.447 24536.191 2 JC+I 11749.817 86 23671.635 23722.019 24011.390 3 JC+G4 11426.892 86 23025.785 23076.169 23365.540 4 JC+I+G4 11409.860 87 22993.720 23045.450 23337.426 5 JC+R2 11538.548 87 23251.096 23302.826 23594.802 6 JC+R3 11416.865 89 23011.730 23066.220 23363.337 7 JC+R4 11408.567 91 22999.135 23056.477 23358.643 8 JC+R5 11407.459 93 23000.917 23061.207 23368.327 14 F81+F 12014.723 88 24205.447 24258.545 24553.103 15 F81+F+I 11746.066 89 23670.131 23724.621 24021.738 16 F81+F+G4 11418.644 89 23015.289 23069.779 23366.896 17 F81+F+I+G4 11401.906 90 22983.812 23039.716 23339.370 18 F81+F+R2 11532.431 90 23244.861 23300.766 23600.419 19 F81+F+R3 11409.624 92 23003.248 23062.052 23366.707 20 F81+F+R4 11399.419 94 22986.839 23048.638 23358.199 21 F81+F+R5 11399.287 96 22990.575 23055.467 23369.836 27 K2P 11970.818 86 24113.636 24164.020 24453.391 28 K2P+I 11705.384 87 23584.767 23636.497 23928.473 29 K2P+G4 11377.365 87 22928.730 22980.460 23272.436 30 K2P+I+G4 11360.860 88 22897.720 22950.818 23245.377 31 K2P+R2 11491.642 88 23159.283 23212.382 23506.940 32 K2P+R3 11368.396 90 22916.792 22972.696 23272.350 33 K2P+R4 11358.063 92 22900.125 22958.930 23263.584 34 K2P+R5 11358.037 94 22904.074 22965.874 23275.435 40 HKY+F 11969.910 89 24117.819 24172.309 24469.426 41 HKY+F+I 11700.293 90 23580.586 23636.490 23936.144 42 HKY+F+G4 11366.737 90 22913.475 22969.379 23269.032 43 HKY+F+I+G4 11350.329 91 22882.659 22940.001 23242.167 44 HKY+F+R2 11483.520 91 23149.039 23206.382 23508.548 45 HKY+F+R3 11358.705 93 22903.410 22963.700 23270.820 46 HKY+F+R4 11347.352 95 22884.703 22948.037 23260.014 47 HKY+F+R5 11347.339 97 22888.678 22955.154 23271.891 53 TNe 11969.088 87 24112.176 24163.906 24455.882 54 TNe+I 11696.852 88 23569.705 23622.803 23917.361 55 TNe+G4 11374.378 88 22924.756 22977.854 23272.412 56 TNe+I+G4 11357.169 89 22892.337 22946.827 23243.945 57 TNe+R2 11489.369 89 23156.738 23211.228 23508.345 58 TNe+R3 11362.661 91 22907.323 22964.665 23266.831 59 TNe+R4 11353.344 93 22892.689 22952.978 23260.098 60 TNe+R5 11353.332 95 22896.664 22959.997 23271.975 66 TN+F 11968.110 90 24116.221 24172.125 24471.779 67 TN+F+I 11690.996 91 23563.992 23621.335 23923.501 68 TN+F+G4 11362.959 91 22907.919 22965.261 23267.427 69 TN+F+I+G4 11345.763 92 22875.526 22934.330 23238.985 70 TN+F+R2 11480.714 92 23145.429 23204.233 23508.888 71 TN+F+R3 11351.854 94 22891.708 22953.507 23263.068 72 TN+F+R4 11341.711 96 22875.421 22940.313 23254.683 73 TN+F+R5 11341.613 98 22879.227 22947.311 23266.390 79 K3P 11955.726 87 24085.452 24137.182 24429.158 80 K3P+I 11689.786 88 23555.572 23608.670 23903.229 81 K3P+G4 11366.551 88 22909.101 22962.200 23256.758 82 K3P+I+G4 11349.411 89 22876.821 22931.311 23228.429 83 K3P+R2 11477.146 89 23132.292 23186.782 23483.899 84 K3P+R3 11357.300 91 22896.599 22953.942 23256.108 85 K3P+R4 11346.132 93 22878.264 22938.554 23245.674 86 K3P+R5 11346.075 95 22882.150 22945.483 23257.461 92 K3Pu+F 11954.797 90 24089.594 24145.498 24445.152 93 K3Pu+F+I 11684.711 91 23551.421 23608.764 23910.930 94 K3Pu+F+G4 11356.428 91 22894.856 22952.198 23254.364 95 K3Pu+F+I+G4 11339.416 92 22862.833 22921.637 23226.292 96 K3Pu+F+R2 11469.398 92 23122.796 23181.600 23486.255 97 K3Pu+F+R3 11348.095 94 22884.191 22945.990 23255.551 98 K3Pu+F+R4 11335.892 96 22863.784 22928.676 23243.046 99 K3Pu+F+R5 11335.816 98 22867.632 22935.716 23254.795 105 TPM2+F 11969.902 90 24119.804 24175.708 24475.361 106 TPM2+F+I 11700.222 91 23582.444 23639.787 23941.953 107 TPM2+F+G4 11365.880 91 22913.760 22971.103 23273.269 108 TPM2+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 109 TPM2+F+R2 11483.376 92 23150.752 23209.556 23514.211 110 TPM2+F+R3 11358.087 94 22904.173 22965.972 23275.533 111 TPM2+F+R4 11346.136 96 22884.272 22949.164 23263.533 112 TPM2+F+R5 11346.063 98 22888.126 22956.210 23275.289 118 TPM2u+F 11969.903 90 24119.805 24175.710 24475.363 119 TPM2u+F+I 11700.223 91 23582.445 23639.788 23941.954 120 TPM2u+F+G4 11365.880 91 22913.760 22971.102 23273.268 121 TPM2u+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 122 TPM2u+F+R2 11483.380 92 23150.760 23209.564 23514.219 123 TPM2u+F+R3 11358.086 94 22904.173 22965.972 23275.533 124 TPM2u+F+R4 11346.012 96 22884.023 22948.915 23263.285 125 TPM2u+F+R5 11346.004 98 22888.009 22956.093 23275.172 131 TPM3+F 11939.208 90 24058.415 24114.320 24413.973 132 TPM3+F+I 11688.861 91 23559.723 23617.065 23919.231 133 TPM3+F+G4 11362.780 91 22907.560 22964.903 23267.069 134 TPM3+F+I+G4 11347.020 92 22878.039 22936.843 23241.498 135 TPM3+F+R2 11476.513 92 23137.026 23195.830 23500.485 136 TPM3+F+R3 11353.918 94 22895.835 22957.634 23267.196 137 TPM3+F+R4 11342.967 96 22877.935 22942.827 23257.196 138 TPM3+F+R5 11342.922 98 22881.844 22949.928 23269.007 144 TPM3u+F 11939.209 90 24058.418 24114.323 24413.976 145 TPM3u+F+I 11688.862 91 23559.723 23617.066 23919.232 146 TPM3u+F+G4 11362.781 91 22907.561 22964.904 23267.070 147 TPM3u+F+I+G4 11347.020 92 22878.040 22936.844 23241.499 148 TPM3u+F+R2 11476.515 92 23137.030 23195.834 23500.489 149 TPM3u+F+R3 11353.918 94 22895.835 22957.634 23267.195 150 TPM3u+F+R4 11342.887 96 22877.774 22942.666 23257.036 151 TPM3u+F+R5 11342.887 98 22881.774 22949.858 23268.937 157 TIMe 11954.065 88 24084.129 24137.228 24431.786 158 TIMe+I 11681.462 89 23540.924 23595.413 23892.531 159 TIMe+G4 11363.653 89 22905.306 22959.796 23256.913 160 TIMe+I+G4 11345.802 90 22871.603 22927.508 23227.161 161 TIMe+R2 11475.095 90 23130.189 23186.094 23485.747 162 TIMe+R3 11351.551 92 22887.101 22945.905 23250.560 163 TIMe+R4 11341.268 94 22870.536 22932.335 23241.896 164 TIMe+R5 11341.264 96 22874.528 22939.420 23253.790 170 TIM+F 11953.073 91 24088.145 24145.488 24447.654 171 TIM+F+I 11675.638 92 23535.276 23594.080 23898.735 172 TIM+F+G4 11352.739 92 22889.478 22948.282 23252.937 173 TIM+F+I+G4 11334.933 93 22855.867 22916.156 23223.276 174 TIM+F+R2 11466.803 93 23119.606 23179.896 23487.016 175 TIM+F+R3 11341.217 95 22872.434 22935.768 23247.745 176 TIM+F+R4 11330.083 97 22854.165 22920.641 23237.378 177 TIM+F+R5 11330.040 99 22858.080 22927.799 23249.194 183 TIM2e 11969.060 88 24114.119 24167.218 24461.776 184 TIM2e+I 11696.724 89 23571.449 23625.939 23923.056 185 TIM2e+G4 11373.751 89 22925.503 22979.993 23277.110 186 TIM2e+I+G4 11356.625 90 22893.250 22949.154 23248.808 187 TIM2e+R2 11489.326 90 23158.651 23214.556 23514.209 188 TIM2e+R3 11362.313 92 22908.626 22967.431 23272.086 189 TIM2e+R4 11352.064 94 22892.128 22953.927 23263.488 190 TIM2e+R5 11352.061 96 22896.122 22961.014 23275.384 196 TIM2+F 11968.103 91 24118.206 24175.549 24477.715 197 TIM2+F+I 11690.924 92 23565.848 23624.653 23929.308 198 TIM2+F+G4 11362.111 92 22908.222 22967.027 23271.682 199 TIM2+F+I+G4 11345.003 93 22876.007 22936.297 23243.417 200 TIM2+F+R2 11480.623 93 23147.246 23207.536 23514.656 201 TIM2+F+R3 11351.348 95 22892.696 22956.029 23268.007 202 TIM2+F+R4 11340.298 97 22874.597 22941.072 23257.809 203 TIM2+F+R5 11340.262 99 22878.523 22948.242 23269.637 209 TIM3e 11929.583 88 24035.165 24088.263 24382.822 210 TIM3e+I 11679.665 89 23537.329 23591.819 23888.937 211 TIM3e+G4 11366.249 89 22910.499 22964.989 23262.106 212 TIM3e+I+G4 11350.100 90 22880.199 22936.104 23235.757 213 TIM3e+R2 11477.347 90 23134.694 23190.598 23490.252 214 TIM3e+R3 11353.723 92 22891.445 22950.249 23254.904 215 TIM3e+R4 11345.129 94 22878.259 22940.058 23249.619 216 TIM3e+R5 11345.116 96 22882.233 22947.125 23261.494 222 TIM3+F 11937.046 91 24056.091 24113.433 24415.599 223 TIM3+F+I 11679.411 92 23542.822 23601.627 23906.282 224 TIM3+F+G4 11358.813 92 22901.625 22960.429 23265.084 225 TIM3+F+I+G4 11342.334 93 22870.668 22930.957 23238.077 226 TIM3+F+R2 11473.687 93 23133.374 23193.664 23500.784 227 TIM3+F+R3 11347.077 95 22884.154 22947.488 23259.465 228 TIM3+F+R4 11337.180 97 22868.361 22934.836 23251.573 229 TIM3+F+R5 11337.160 99 22872.319 22942.037 23263.433 235 TVMe 11915.914 89 24009.828 24064.317 24361.435 236 TVMe+I 11672.235 90 23524.469 23580.374 23880.027 237 TVMe+G4 11355.962 90 22891.924 22947.828 23247.481 238 TVMe+I+G4 11340.052 91 22862.103 22919.446 23221.612 239 TVMe+R2 11464.332 91 23110.664 23168.006 23470.172 240 TVMe+R3 11345.869 93 22877.738 22938.028 23245.148 241 TVMe+R4 11336.465 95 22862.930 22926.264 23238.241 242 TVMe+R5 11336.449 97 22866.898 22933.374 23250.111 248 TVM+F 11923.307 92 24030.614 24089.418 24394.073 249 TVM+F+I 11672.689 93 23531.379 23591.668 23898.789 250 TVM+F+G4 11349.481 93 22884.961 22945.251 23252.371 251 TVM+F+I+G4 11333.273 94 22854.547 22916.346 23225.907 252 TVM+F+R2 11461.206 94 23110.412 23172.211 23481.772 253 TVM+F+R3 11340.584 96 22873.169 22938.061 23252.431 254 TVM+F+R4 11329.650 98 22855.299 22923.383 23242.462 255 TVM+F+R5 11329.621 100 22859.241 22930.619 23254.305 261 SYM 11913.886 90 24007.771 24063.676 24363.329 262 SYM+I 11663.801 91 23509.602 23566.945 23869.111 263 SYM+G4 11352.816 91 22887.633 22944.975 23247.141 264 SYM+I+G4 11336.290 92 22856.581 22915.385 23220.040 265 SYM+R2 11462.111 92 23108.223 23167.027 23471.682 266 SYM+R3 11340.196 94 22868.392 22930.192 23239.753 267 SYM+R4 11332.021 96 22856.043 22920.935 23235.305 268 SYM+R5 11332.007 98 22860.014 22928.098 23247.177 274 GTR+F 11921.235 93 24028.470 24088.759 24395.880 275 GTR+F+I 11663.491 94 23514.983 23576.782 23886.343 276 GTR+F+G4 11345.623 94 22879.246 22941.045 23250.606 277 GTR+F+I+G4 11328.789 95 22847.578 22910.912 23222.890 278 GTR+F+R2 11458.594 95 23107.189 23170.522 23482.500 279 GTR+F+R3 11333.883 97 22861.767 22928.242 23244.979 280 GTR+F+R4 11324.370 99 22846.739 22916.457 23237.853 281 GTR+F+R5 11324.349 101 22850.699 22923.762 23249.713 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: SYM+I+G4 Best-fit model: SYM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 44.294 seconds (0h:0m:44s) Wall-clock time for ModelFinder: 66.960 seconds (0h:1m:6s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.872 / LogL: -11352.830 Init pinv, alpha: 0.012, 1.000 / Estimate: 0.086, 1.479 / LogL: -11336.284 Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.484 / LogL: -11336.280 Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.486 / LogL: -11336.278 Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.485 / LogL: -11336.279 Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.487 / LogL: -11336.278 Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.488 / LogL: -11336.278 Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.490 / LogL: -11336.278 Optimal pinv,alpha: 0.087, 1.488 / LogL: -11336.278 Parameters optimization took 4.570 sec Computing ML distances based on estimated model parameters... 0.028 sec Computing BIONJ tree... 0.003 seconds Log-likelihood of BIONJ tree: -11256.524 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 1.788 second Computing log-likelihood of 98 initial trees ... 5.003 seconds Current best score: -11232.454 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11229.757 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11224.589 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 4: -11222.746 Iteration 10 / LogL: -11224.681 / Time: 0h:0m:16s Iteration 20 / LogL: -11224.683 / Time: 0h:0m:19s Finish initializing candidate tree set (13) Current best tree score: -11222.746 / CPU time: 15.000 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11223.099 / Time: 0h:0m:24s (0h:1m:3s left) Iteration 40 / LogL: -11222.967 / Time: 0h:0m:31s (0h:0m:50s left) Iteration 50 / LogL: -11223.103 / Time: 0h:0m:39s (0h:0m:43s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 58: -11222.586 Iteration 60 / LogL: -11222.964 / Time: 0h:0m:45s (0h:1m:15s left) Iteration 70 / LogL: -11222.613 / Time: 0h:0m:49s (0h:1m:3s left) Iteration 80 / LogL: -11222.617 / Time: 0h:0m:54s (0h:0m:53s left) Iteration 90 / LogL: -11222.729 / Time: 0h:1m:1s (0h:0m:47s left) Iteration 100 / LogL: -11222.896 / Time: 0h:1m:5s (0h:0m:38s left) Iteration 110 / LogL: -11222.658 / Time: 0h:1m:11s (0h:0m:31s left) Iteration 120 / LogL: -11222.911 / Time: 0h:1m:18s (0h:0m:24s left) Iteration 130 / LogL: -11226.630 / Time: 0h:1m:24s (0h:0m:18s left) Iteration 140 / LogL: -11222.794 / Time: 0h:1m:27s (0h:0m:11s left) Iteration 150 / LogL: -11223.523 / Time: 0h:1m:33s (0h:0m:5s left) TREE SEARCH COMPLETED AFTER 159 ITERATIONS / Time: 0h:1m:39s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.586 Optimal log-likelihood: -11222.578 Rate parameters: A-C: 1.61120 A-G: 2.49430 A-T: 1.81454 C-G: 2.16728 C-T: 2.95194 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.566 Parameters optimization took 1 rounds (0.206 sec) BEST SCORE FOUND : -11222.578 Total tree length: 12.512 Total number of iterations: 159 CPU time used for tree search: 58.903 sec (0h:0m:58s) Wall-clock time used for tree search: 94.235 sec (0h:1m:34s) Total CPU time used: 62.764 sec (0h:1m:2s) Total wall-clock time used: 99.299 sec (0h:1m:39s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Sun Jul 4 03:41:17 2021 real 2m46.363s user 1m47.083s sys 0m1.206s + /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo IQ-TREE multicore version 1.6.9 for Linux 64-bit built Jan 2 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: i-capture-the-hostname (AVX, 47 GB RAM) Command: /build/iqtree-1.6.9+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo Seed: 13070 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sun Jul 4 03:41:18 2021 Kernel: AVX - 2 threads (15 CPU cores detected) Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: Restoring information from model checkpoint file example.phy.model.gz CHECKPOINT: Initial tree restored NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 JC 12015.193 85 24200.386 24249.447 24536.191 2 JC+I 11749.817 86 23671.635 23722.019 24011.390 3 JC+G4 11426.892 86 23025.785 23076.169 23365.540 4 JC+I+G4 11409.860 87 22993.720 23045.450 23337.426 5 JC+R2 11538.548 87 23251.096 23302.826 23594.802 6 JC+R3 11416.865 89 23011.730 23066.220 23363.337 7 JC+R4 11408.567 91 22999.135 23056.477 23358.643 8 JC+R5 11407.459 93 23000.917 23061.207 23368.327 14 F81+F 12014.723 88 24205.447 24258.545 24553.103 15 F81+F+I 11746.066 89 23670.131 23724.621 24021.738 16 F81+F+G4 11418.644 89 23015.289 23069.779 23366.896 17 F81+F+I+G4 11401.906 90 22983.812 23039.716 23339.370 18 F81+F+R2 11532.431 90 23244.861 23300.766 23600.419 19 F81+F+R3 11409.624 92 23003.248 23062.052 23366.707 20 F81+F+R4 11399.419 94 22986.839 23048.638 23358.199 21 F81+F+R5 11399.287 96 22990.575 23055.467 23369.836 27 K2P 11970.818 86 24113.636 24164.020 24453.391 28 K2P+I 11705.384 87 23584.767 23636.497 23928.473 29 K2P+G4 11377.365 87 22928.730 22980.460 23272.436 30 K2P+I+G4 11360.860 88 22897.720 22950.818 23245.377 31 K2P+R2 11491.642 88 23159.283 23212.382 23506.940 32 K2P+R3 11368.396 90 22916.792 22972.696 23272.350 33 K2P+R4 11358.063 92 22900.125 22958.930 23263.584 34 K2P+R5 11358.037 94 22904.074 22965.874 23275.435 40 HKY+F 11969.910 89 24117.819 24172.309 24469.426 41 HKY+F+I 11700.293 90 23580.586 23636.490 23936.144 42 HKY+F+G4 11366.737 90 22913.475 22969.379 23269.032 43 HKY+F+I+G4 11350.329 91 22882.659 22940.001 23242.167 44 HKY+F+R2 11483.520 91 23149.039 23206.382 23508.548 45 HKY+F+R3 11358.705 93 22903.410 22963.700 23270.820 46 HKY+F+R4 11347.352 95 22884.703 22948.037 23260.014 47 HKY+F+R5 11347.339 97 22888.678 22955.154 23271.891 53 TNe 11969.088 87 24112.176 24163.906 24455.882 54 TNe+I 11696.852 88 23569.705 23622.803 23917.361 55 TNe+G4 11374.378 88 22924.756 22977.854 23272.412 56 TNe+I+G4 11357.169 89 22892.337 22946.827 23243.945 57 TNe+R2 11489.369 89 23156.738 23211.228 23508.345 58 TNe+R3 11362.661 91 22907.323 22964.665 23266.831 59 TNe+R4 11353.344 93 22892.689 22952.978 23260.098 60 TNe+R5 11353.332 95 22896.664 22959.997 23271.975 66 TN+F 11968.110 90 24116.221 24172.125 24471.779 67 TN+F+I 11690.996 91 23563.992 23621.335 23923.501 68 TN+F+G4 11362.959 91 22907.919 22965.261 23267.427 69 TN+F+I+G4 11345.763 92 22875.526 22934.330 23238.985 70 TN+F+R2 11480.714 92 23145.429 23204.233 23508.888 71 TN+F+R3 11351.854 94 22891.708 22953.507 23263.068 72 TN+F+R4 11341.711 96 22875.421 22940.313 23254.683 73 TN+F+R5 11341.613 98 22879.227 22947.311 23266.390 79 K3P 11955.726 87 24085.452 24137.182 24429.158 80 K3P+I 11689.786 88 23555.572 23608.670 23903.229 81 K3P+G4 11366.551 88 22909.101 22962.200 23256.758 82 K3P+I+G4 11349.411 89 22876.821 22931.311 23228.429 83 K3P+R2 11477.146 89 23132.292 23186.782 23483.899 84 K3P+R3 11357.300 91 22896.599 22953.942 23256.108 85 K3P+R4 11346.132 93 22878.264 22938.554 23245.674 86 K3P+R5 11346.075 95 22882.150 22945.483 23257.461 92 K3Pu+F 11954.797 90 24089.594 24145.498 24445.152 93 K3Pu+F+I 11684.711 91 23551.421 23608.764 23910.930 94 K3Pu+F+G4 11356.428 91 22894.856 22952.198 23254.364 95 K3Pu+F+I+G4 11339.416 92 22862.833 22921.637 23226.292 96 K3Pu+F+R2 11469.398 92 23122.796 23181.600 23486.255 97 K3Pu+F+R3 11348.095 94 22884.191 22945.990 23255.551 98 K3Pu+F+R4 11335.892 96 22863.784 22928.676 23243.046 99 K3Pu+F+R5 11335.816 98 22867.632 22935.716 23254.795 105 TPM2+F 11969.902 90 24119.804 24175.708 24475.361 106 TPM2+F+I 11700.222 91 23582.444 23639.787 23941.953 107 TPM2+F+G4 11365.880 91 22913.760 22971.103 23273.269 108 TPM2+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 109 TPM2+F+R2 11483.376 92 23150.752 23209.556 23514.211 110 TPM2+F+R3 11358.087 94 22904.173 22965.972 23275.533 111 TPM2+F+R4 11346.136 96 22884.272 22949.164 23263.533 112 TPM2+F+R5 11346.063 98 22888.126 22956.210 23275.289 118 TPM2u+F 11969.903 90 24119.805 24175.710 24475.363 119 TPM2u+F+I 11700.223 91 23582.445 23639.788 23941.954 120 TPM2u+F+G4 11365.880 91 22913.760 22971.102 23273.268 121 TPM2u+F+I+G4 11349.479 92 22882.958 22941.762 23246.417 122 TPM2u+F+R2 11483.380 92 23150.760 23209.564 23514.219 123 TPM2u+F+R3 11358.086 94 22904.173 22965.972 23275.533 124 TPM2u+F+R4 11346.012 96 22884.023 22948.915 23263.285 125 TPM2u+F+R5 11346.004 98 22888.009 22956.093 23275.172 131 TPM3+F 11939.208 90 24058.415 24114.320 24413.973 132 TPM3+F+I 11688.861 91 23559.723 23617.065 23919.231 133 TPM3+F+G4 11362.780 91 22907.560 22964.903 23267.069 134 TPM3+F+I+G4 11347.020 92 22878.039 22936.843 23241.498 135 TPM3+F+R2 11476.513 92 23137.026 23195.830 23500.485 136 TPM3+F+R3 11353.918 94 22895.835 22957.634 23267.196 137 TPM3+F+R4 11342.967 96 22877.935 22942.827 23257.196 138 TPM3+F+R5 11342.922 98 22881.844 22949.928 23269.007 144 TPM3u+F 11939.209 90 24058.418 24114.323 24413.976 145 TPM3u+F+I 11688.862 91 23559.723 23617.066 23919.232 146 TPM3u+F+G4 11362.781 91 22907.561 22964.904 23267.070 147 TPM3u+F+I+G4 11347.020 92 22878.040 22936.844 23241.499 148 TPM3u+F+R2 11476.515 92 23137.030 23195.834 23500.489 149 TPM3u+F+R3 11353.918 94 22895.835 22957.634 23267.195 150 TPM3u+F+R4 11342.887 96 22877.774 22942.666 23257.036 151 TPM3u+F+R5 11342.887 98 22881.774 22949.858 23268.937 157 TIMe 11954.065 88 24084.129 24137.228 24431.786 158 TIMe+I 11681.462 89 23540.924 23595.413 23892.531 159 TIMe+G4 11363.653 89 22905.306 22959.796 23256.913 160 TIMe+I+G4 11345.802 90 22871.603 22927.508 23227.161 161 TIMe+R2 11475.095 90 23130.189 23186.094 23485.747 162 TIMe+R3 11351.551 92 22887.101 22945.905 23250.560 163 TIMe+R4 11341.268 94 22870.536 22932.335 23241.896 164 TIMe+R5 11341.264 96 22874.528 22939.420 23253.790 170 TIM+F 11953.073 91 24088.145 24145.488 24447.654 171 TIM+F+I 11675.638 92 23535.276 23594.080 23898.735 172 TIM+F+G4 11352.739 92 22889.478 22948.282 23252.937 173 TIM+F+I+G4 11334.933 93 22855.867 22916.156 23223.276 174 TIM+F+R2 11466.803 93 23119.606 23179.896 23487.016 175 TIM+F+R3 11341.217 95 22872.434 22935.768 23247.745 176 TIM+F+R4 11330.083 97 22854.165 22920.641 23237.378 177 TIM+F+R5 11330.040 99 22858.080 22927.799 23249.194 183 TIM2e 11969.060 88 24114.119 24167.218 24461.776 184 TIM2e+I 11696.724 89 23571.449 23625.939 23923.056 185 TIM2e+G4 11373.751 89 22925.503 22979.993 23277.110 186 TIM2e+I+G4 11356.625 90 22893.250 22949.154 23248.808 187 TIM2e+R2 11489.326 90 23158.651 23214.556 23514.209 188 TIM2e+R3 11362.313 92 22908.626 22967.431 23272.086 189 TIM2e+R4 11352.064 94 22892.128 22953.927 23263.488 190 TIM2e+R5 11352.061 96 22896.122 22961.014 23275.384 196 TIM2+F 11968.103 91 24118.206 24175.549 24477.715 197 TIM2+F+I 11690.924 92 23565.848 23624.653 23929.308 198 TIM2+F+G4 11362.111 92 22908.222 22967.027 23271.682 199 TIM2+F+I+G4 11345.003 93 22876.007 22936.297 23243.417 200 TIM2+F+R2 11480.623 93 23147.246 23207.536 23514.656 201 TIM2+F+R3 11351.348 95 22892.696 22956.029 23268.007 202 TIM2+F+R4 11340.298 97 22874.597 22941.072 23257.809 203 TIM2+F+R5 11340.262 99 22878.523 22948.242 23269.637 209 TIM3e 11929.583 88 24035.165 24088.263 24382.822 210 TIM3e+I 11679.665 89 23537.329 23591.819 23888.937 211 TIM3e+G4 11366.249 89 22910.499 22964.989 23262.106 212 TIM3e+I+G4 11350.100 90 22880.199 22936.103 23235.757 213 TIM3e+R2 11477.347 90 23134.694 23190.598 23490.252 214 TIM3e+R3 11353.723 92 22891.445 22950.249 23254.904 215 TIM3e+R4 11345.129 94 22878.259 22940.058 23249.619 216 TIM3e+R5 11345.116 96 22882.233 22947.125 23261.494 222 TIM3+F 11937.046 91 24056.091 24113.433 24415.599 223 TIM3+F+I 11679.411 92 23542.822 23601.627 23906.282 224 TIM3+F+G4 11358.813 92 22901.625 22960.429 23265.084 225 TIM3+F+I+G4 11342.334 93 22870.668 22930.957 23238.077 226 TIM3+F+R2 11473.687 93 23133.374 23193.664 23500.784 227 TIM3+F+R3 11347.077 95 22884.154 22947.488 23259.465 228 TIM3+F+R4 11337.180 97 22868.361 22934.836 23251.573 229 TIM3+F+R5 11337.160 99 22872.319 22942.037 23263.433 235 TVMe 11915.914 89 24009.828 24064.317 24361.435 236 TVMe+I 11672.235 90 23524.469 23580.374 23880.027 237 TVMe+G4 11355.962 90 22891.924 22947.828 23247.481 238 TVMe+I+G4 11340.052 91 22862.103 22919.446 23221.612 239 TVMe+R2 11464.332 91 23110.664 23168.006 23470.172 240 TVMe+R3 11345.869 93 22877.738 22938.028 23245.148 241 TVMe+R4 11336.465 95 22862.930 22926.264 23238.242 242 TVMe+R5 11336.449 97 22866.898 22933.374 23250.111 248 TVM+F 11923.307 92 24030.614 24089.418 24394.073 249 TVM+F+I 11672.689 93 23531.379 23591.668 23898.789 250 TVM+F+G4 11349.481 93 22884.961 22945.251 23252.371 251 TVM+F+I+G4 11333.273 94 22854.547 22916.346 23225.907 252 TVM+F+R2 11461.206 94 23110.412 23172.211 23481.772 253 TVM+F+R3 11340.584 96 22873.169 22938.061 23252.431 254 TVM+F+R4 11329.650 98 22855.299 22923.383 23242.462 255 TVM+F+R5 11329.621 100 22859.241 22930.619 23254.305 261 SYM 11913.886 90 24007.771 24063.676 24363.329 262 SYM+I 11663.801 91 23509.602 23566.945 23869.111 263 SYM+G4 11352.816 91 22887.633 22944.975 23247.141 264 SYM+I+G4 11336.290 92 22856.581 22915.385 23220.040 265 SYM+R2 11462.111 92 23108.223 23167.027 23471.682 266 SYM+R3 11340.196 94 22868.392 22930.192 23239.753 267 SYM+R4 11332.021 96 22856.043 22920.935 23235.305 268 SYM+R5 11332.007 98 22860.014 22928.098 23247.177 274 GTR+F 11921.235 93 24028.470 24088.759 24395.880 275 GTR+F+I 11663.491 94 23514.982 23576.782 23886.343 276 GTR+F+G4 11345.623 94 22879.246 22941.045 23250.606 277 GTR+F+I+G4 11328.789 95 22847.578 22910.912 23222.890 278 GTR+F+R2 11458.594 95 23107.189 23170.522 23482.500 279 GTR+F+R3 11333.883 97 22861.767 22928.242 23244.979 280 GTR+F+R4 11324.370 99 22846.739 22916.457 23237.853 281 GTR+F+R5 11324.349 101 22850.699 22923.762 23249.713 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: GTR+F+I+G4 Bayesian Information Criterion: SYM+I+G4 Best-fit model: SYM+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 0.087 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.192 seconds (0h:0m:0s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.872 / LogL: -11352.830 Init pinv, alpha: 0.012, 1.000 / Estimate: 0.086, 1.479 / LogL: -11336.284 Init pinv, alpha: 0.023, 1.000 / Estimate: 0.087, 1.484 / LogL: -11336.280 Init pinv, alpha: 0.035, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 Init pinv, alpha: 0.046, 1.000 / Estimate: 0.087, 1.486 / LogL: -11336.278 Init pinv, alpha: 0.058, 1.000 / Estimate: 0.087, 1.481 / LogL: -11336.282 Init pinv, alpha: 0.069, 1.000 / Estimate: 0.087, 1.485 / LogL: -11336.279 Init pinv, alpha: 0.081, 1.000 / Estimate: 0.087, 1.487 / LogL: -11336.278 Init pinv, alpha: 0.093, 1.000 / Estimate: 0.087, 1.488 / LogL: -11336.278 Init pinv, alpha: 0.104, 1.000 / Estimate: 0.087, 1.490 / LogL: -11336.278 Optimal pinv,alpha: 0.087, 1.488 / LogL: -11336.278 Parameters optimization took 12.412 sec Computing ML distances based on estimated model parameters... 0.040 sec Computing BIONJ tree... 0.002 seconds Log-likelihood of BIONJ tree: -11256.524 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 2.427 second Computing log-likelihood of 98 initial trees ... 6.947 seconds Current best score: -11234.904 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11229.869 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11224.594 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 4: -11224.232 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 6: -11223.763 Iteration 10 / LogL: -11229.722 / Time: 0h:0m:27s Iteration 20 / LogL: -11229.422 / Time: 0h:0m:31s Finish initializing candidate tree set (12) Current best tree score: -11223.763 / CPU time: 18.918 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 25: -11222.142 Iteration 30 / LogL: -11222.205 / Time: 0h:0m:40s (0h:2m:14s left) Iteration 40 / LogL: -11222.184 / Time: 0h:0m:52s (0h:1m:54s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 42: -11221.575 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 46: -11221.030 Iteration 50 / LogL: -11228.112 / Time: 0h:0m:59s (0h:1m:56s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 57: -11220.891 Iteration 60 / LogL: -11220.923 / Time: 0h:1m:1s (0h:1m:41s left) Iteration 70 / LogL: -11220.898 / Time: 0h:1m:4s (0h:1m:21s left) Iteration 80 / LogL: -11221.060 / Time: 0h:1m:12s (0h:1m:10s left) Iteration 90 / LogL: -11221.868 / Time: 0h:1m:29s (0h:1m:7s left) Iteration 100 / LogL: -11221.110 / Time: 0h:1m:42s (0h:0m:59s left) Iteration 110 / LogL: -11221.725 / Time: 0h:1m:55s (0h:0m:49s left) Iteration 120 / LogL: -11220.893 / Time: 0h:2m:18s (0h:0m:43s left) Iteration 130 / LogL: -11221.227 / Time: 0h:2m:44s (0h:0m:34s left) Iteration 140 / LogL: -11221.052 / Time: 0h:2m:50s (0h:0m:20s left) Iteration 150 / LogL: -11225.796 / Time: 0h:3m:12s (0h:0m:9s left) TREE SEARCH COMPLETED AFTER 158 ITERATIONS / Time: 0h:3m:33s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11220.891 Optimal log-likelihood: -11220.890 Rate parameters: A-C: 1.52469 A-G: 2.42492 A-T: 1.66566 C-G: 1.99473 C-T: 2.82957 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.533 Parameters optimization took 1 rounds (0.255 sec) BEST SCORE FOUND : -11220.890 Total tree length: 12.593 Total number of iterations: 158 CPU time used for tree search: 192.886 sec (0h:3m:12s) Wall-clock time used for tree search: 200.912 sec (0h:3m:20s) Total CPU time used: 204.959 sec (0h:3m:24s) Total wall-clock time used: 213.846 sec (0h:3m:33s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Sun Jul 4 03:44:52 2021 real 3m34.130s user 3m25.085s sys 0m1.825s + rm -rf /tmp/iqtree-test.G6Cjoh 312.21user 3.04system 6:20.81elapsed 82%CPU (0avgtext+0avgdata 14944maxresident)k 752inputs+0outputs (21major+6708minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_auto_install -Bbuild.omp cd build.omp && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make 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'/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 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 make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/alignment /build/iqtree-1.6.9+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/pda /build/iqtree-1.6.9+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 26%] Built target kernelavx [ 42%] Built target pll [ 43%] Built target kernelfma [ 44%] Built target kernelsse [ 49%] Built target utils [ 55%] Built target whtest make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/model /build/iqtree-1.6.9+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 64%] Built target pda [ 68%] Built target alignment make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/tree /build/iqtree-1.6.9+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' cd /build/iqtree-1.6.9+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' [ 98%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-1.6.9+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-1.6.9+dfsg/lib -Wl,-rpath,/build/iqtree-1.6.9+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.omp/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.omp' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.omp' dh_auto_install -Bbuild.serial cd build.serial && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/gsl /build/iqtree-1.6.9+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/ncl /build/iqtree-1.6.9+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb /build/iqtree-1.6.9+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pll /build/iqtree-1.6.9+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/nclextra /build/iqtree-1.6.9+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/whtest /build/iqtree-1.6.9+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/sprng /build/iqtree-1.6.9+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/vectorclass /build/iqtree-1.6.9+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build [ 2%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/utils /build/iqtree-1.6.9+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 3%] Built target vectorclass make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 7%] Built target gsl [ 8%] Built target pllavx make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build [ 12%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 15%] Built target nclextra 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-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/pda /build/iqtree-1.6.9+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/alignment /build/iqtree-1.6.9+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 41%] Built target pll make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 42%] Built target kernelavx [ 43%] Built target kernelfma make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 44%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 50%] Built target whtest make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 55%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 59%] Built target alignment [ 68%] Built target pda make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/model /build/iqtree-1.6.9+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/tree /build/iqtree-1.6.9+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' cd /build/iqtree-1.6.9+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.serial/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.serial' dh_auto_install -Bbuild.mpi cd build.mpi && make -j15 install DESTDIR=/build/iqtree-1.6.9\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-1.6.9+dfsg -B/build/iqtree-1.6.9+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/mympi.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/gsl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/gsl /build/iqtree-1.6.9+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/ncl /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/ncl /build/iqtree-1.6.9+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb /build/iqtree-1.6.9+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pll /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pll /build/iqtree-1.6.9+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/nclextra /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/nclextra /build/iqtree-1.6.9+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/whtest /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/whtest /build/iqtree-1.6.9+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/sprng /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/sprng /build/iqtree-1.6.9+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass /build/iqtree-1.6.9+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 1%] Built target lbfgsb make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend [ 2%] Built target vectorclass make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/utils /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/utils /build/iqtree-1.6.9+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build [ 6%] Built target gsl [ 10%] Built target sprng make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/mympi.dir/build.make CMakeFiles/mympi.dir/build make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 13%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend [ 14%] Built target pllavx [ 24%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/pda /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/pda /build/iqtree-1.6.9+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/alignment /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/alignment /build/iqtree-1.6.9+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 25%] Built target kernelavx [ 26%] Built target kernelfma [ 27%] Built target kernelsse make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/mympi.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 28%] Built target mympi make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 43%] Built target pll make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 49%] Built target whtest [ 54%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 63%] Built target pda [ 67%] Built target alignment make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/model /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/model /build/iqtree-1.6.9+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/tree /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/tree /build/iqtree-1.6.9+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' cd /build/iqtree-1.6.9+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-1.6.9+dfsg/build.mpi/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-1.6.9+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi -- Set runtime path of "/build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi" to "" -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-1.6.9+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' dh_install find debian -name iqtree-mpi -exec chrpath --delete \{\} \; find debian -name iqtree-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/iqtree-1.6.9+dfsg' mkdir -p /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-omp > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.9+dfsg" /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/bin/iqtree-mpi > /build/iqtree-1.6.9+dfsg/debian/iqtree/usr/share/man/man1//iqtree-mpi.1 make[1]: Leaving directory '/build/iqtree-1.6.9+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_1.6.9+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree' in '../iqtree_1.6.9+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../iqtree_1.6.9+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/42517/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/42517/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/42517 and its subdirectories I: Current time: Sun Jul 4 03:47:02 +14 2021 I: pbuilder-time-stamp: 1625320022