I: pbuilder: network access will be disabled during build I: Current time: Tue Apr 25 16:42:58 +14 2023 I: pbuilder-time-stamp: 1682390578 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. 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_2.0.7+dfsg-1.dsc] I: copying [./iqtree_2.0.7+dfsg.orig.tar.xz] I: copying [./iqtree_2.0.7+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Jan 22 04:08:08 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iqtree_2.0.7+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting iqtree in iqtree-2.0.7+dfsg dpkg-source: info: unpacking iqtree_2.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/446769/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-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 '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Apr 25 16:43 /bin/sh -> /bin/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/446769/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/446769/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(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=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=65c472d7c0a54ba49ad29c9e856292f9 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=446769 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/r-b-build.aPoyGWrE/pbuilderrc_v8O6 --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b2 --logfile b2/build.log --extrapackages usrmerge iqtree_2.0.7+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 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 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Feb 13 10:05 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Feb 13 10:05 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 25 16:43 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/446769/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-compat (= 13), cmake, libboost-dev, 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 ... 19596 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev 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} bsdextrautils{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} gfortran-12{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libbsd0{a} libcbor0.8{a} libcurl4{a} libdebhelper-perl{a} libedit2{a} libeigen3-dev{a} libelf1{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-12-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} libldap-2.5-0{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1{a} libmunge2{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} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libproc2-0{a} libpsl5{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsprng2{a} libsprng2-dev{a} libssh2-1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libucx0{a} libuv1{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{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} pkgconf{a} pkgconf-bin{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 javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget xauth 0 packages upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 71.1 MB of archives. After unpacking 381 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2 [988 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-8 [386 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 41 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 48 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libgfortran-12-dev amd64 12.2.0-14 [834 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 gfortran-12 amd64 12.2.0-14 [10.2 MB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 help2man amd64 1.49.3 [198 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libevent-2.1-7 amd64 2.1.12-stable-8 [180 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libevent-extra-2.1-7 amd64 2.1.12-stable-8 [107 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libevent-openssl-2.1-7 amd64 2.1.12-stable-8 [60.6 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libevent-dev amd64 2.1.12-stable-8 [305 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libgmpxx4ldbl amd64 2:6.2.1+dfsg1-1.1 [338 kB] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libgmp-dev amd64 2:6.2.1+dfsg1-1.1 [641 kB] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libnuma-dev amd64 2.0.16-1 [35.0 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libltdl7 amd64 2.4.7-5 [393 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libltdl-dev amd64 2.4.7-5 [164 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 libhwloc-dev amd64 2.9.0-1 [241 kB] Get: 89 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get: 90 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get: 91 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get: 92 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get: 93 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2 [292 kB] Get: 94 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2 [759 kB] Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-1 [13.3 kB] Get: 97 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get: 98 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get: 99 http://deb.debian.org/debian bookworm/main amd64 libnl-3-dev amd64 3.7.0-0.2+b1 [104 kB] Get: 100 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-dev amd64 3.7.0-0.2+b1 [203 kB] Get: 101 http://deb.debian.org/debian bookworm/main amd64 libibverbs-dev amd64 44.0-2 [633 kB] Get: 102 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 103 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 104 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get: 105 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get: 106 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get: 107 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get: 108 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get: 109 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 110 http://deb.debian.org/debian bookworm/main amd64 libpmix-dev amd64 4.2.2-1+b1 [902 kB] Get: 111 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 112 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 113 http://deb.debian.org/debian bookworm/main amd64 libsprng2 amd64 2.0a-13 [75.8 kB] Get: 114 http://deb.debian.org/debian bookworm/main amd64 libsprng2-dev amd64 2.0a-13 [77.9 kB] Get: 115 http://deb.debian.org/debian bookworm/main amd64 mpi-default-dev amd64 1.14 [5548 B] Get: 116 http://deb.debian.org/debian bookworm/main amd64 time amd64 1.9-0.2 [50.8 kB] Fetched 71.1 MB in 3s (25.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_amd64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_amd64.deb ... Unpacking libmagic1:amd64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_amd64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_amd64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../008-libuchardet0_0.0.7-1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_amd64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_amd64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../011-libpipeline1_1.5.7-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_amd64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../013-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../014-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../015-libcbor0.8_0.8.0-2+b1_amd64.deb ... Unpacking libcbor0.8:amd64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:amd64. Preparing to unpack .../016-libfido2-1_1.12.0-2+b1_amd64.deb ... Unpacking libfido2-1:amd64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../017-openssh-client_1%3a9.2p1-2_amd64.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-3_amd64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../022-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package chrpath. Preparing to unpack .../023-chrpath_0.16-2+b1_amd64.deb ... Unpacking chrpath (0.16-2+b1) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../024-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../025-libxml2_2.9.14+dfsg-1.2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:amd64. Preparing to unpack .../026-libarchive13_3.6.2-1_amd64.deb ... Unpacking libarchive13:amd64 (3.6.2-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../027-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg-10_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../030-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../031-libnghttp2-14_1.52.0-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.52.0-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../032-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../034-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../035-libcurl4_7.88.1-8_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-8) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../036-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../037-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../038-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../039-libuv1_1.44.2-1_amd64.deb ... Unpacking libuv1:amd64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../040-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../041-cmake_3.25.1-1_amd64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../046-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../047-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../048-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../049-libelf1_0.188-2.1_amd64.deb ... Unpacking libelf1:amd64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../050-dwz_0.15-1_amd64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../051-gettext_0.21-12_amd64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../052-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../053-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../054-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../055-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran-12-dev:amd64. Preparing to unpack .../056-libgfortran-12-dev_12.2.0-14_amd64.deb ... Unpacking libgfortran-12-dev:amd64 (12.2.0-14) ... Selecting previously unselected package gfortran-12. Preparing to unpack .../057-gfortran-12_12.2.0-14_amd64.deb ... Unpacking gfortran-12 (12.2.0-14) ... Selecting previously unselected package help2man. Preparing to unpack .../058-help2man_1.49.3_amd64.deb ... Unpacking help2man (1.49.3) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../059-libnl-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../060-libnl-route-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../061-libibverbs1_44.0-2_amd64.deb ... Unpacking libibverbs1:amd64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../062-ibverbs-providers_44.0-2_amd64.deb ... Unpacking ibverbs-providers:amd64 (44.0-2) ... Selecting previously unselected package libboost1.74-dev:amd64. Preparing to unpack .../063-libboost1.74-dev_1.74.0+ds1-20_amd64.deb ... Unpacking libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libboost-dev:amd64. Preparing to unpack .../064-libboost-dev_1.74.0.3_amd64.deb ... Unpacking libboost-dev:amd64 (1.74.0.3) ... Selecting previously unselected package libpkgconf3:amd64. Preparing to unpack .../065-libpkgconf3_1.8.1-1_amd64.deb ... Unpacking libpkgconf3:amd64 (1.8.1-1) ... Selecting previously unselected package pkgconf-bin. Preparing to unpack .../066-pkgconf-bin_1.8.1-1_amd64.deb ... Unpacking pkgconf-bin (1.8.1-1) ... Selecting previously unselected package pkgconf:amd64. Preparing to unpack .../067-pkgconf_1.8.1-1_amd64.deb ... Unpacking pkgconf:amd64 (1.8.1-1) ... Selecting previously unselected package pkg-config:amd64. Preparing to unpack .../068-pkg-config_1.8.1-1_amd64.deb ... Unpacking pkg-config:amd64 (1.8.1-1) ... Selecting previously unselected package libeigen3-dev. Preparing to unpack .../069-libeigen3-dev_3.4.0-4_all.deb ... Unpacking libeigen3-dev (3.4.0-4) ... Selecting previously unselected package libevent-2.1-7:amd64. Preparing to unpack .../070-libevent-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../071-libevent-core-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-extra-2.1-7:amd64. Preparing to unpack .../072-libevent-extra-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../073-libevent-pthreads-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-openssl-2.1-7:amd64. Preparing to unpack .../074-libevent-openssl-2.1-7_2.1.12-stable-8_amd64.deb ... Unpacking libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Selecting previously unselected package libevent-dev. Preparing to unpack .../075-libevent-dev_2.1.12-stable-8_amd64.deb ... Unpacking libevent-dev (2.1.12-stable-8) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../076-libpsm-infinipath1_3.3+20.604758e7-6.2_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../077-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../078-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../079-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../080-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libgmpxx4ldbl:amd64. Preparing to unpack .../081-libgmpxx4ldbl_2%3a6.2.1+dfsg1-1.1_amd64.deb ... Unpacking libgmpxx4ldbl:amd64 (2:6.2.1+dfsg1-1.1) ... Selecting previously unselected package libgmp-dev:amd64. Preparing to unpack .../082-libgmp-dev_2%3a6.2.1+dfsg1-1.1_amd64.deb ... Unpacking libgmp-dev:amd64 (2:6.2.1+dfsg1-1.1) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../083-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libnuma-dev:amd64. Preparing to unpack .../084-libnuma-dev_2.0.16-1_amd64.deb ... Unpacking libnuma-dev:amd64 (2.0.16-1) ... Selecting previously unselected package libltdl7:amd64. Preparing to unpack .../085-libltdl7_2.4.7-5_amd64.deb ... Unpacking libltdl7:amd64 (2.4.7-5) ... Selecting previously unselected package libltdl-dev:amd64. Preparing to unpack .../086-libltdl-dev_2.4.7-5_amd64.deb ... Unpacking libltdl-dev:amd64 (2.4.7-5) ... Selecting previously unselected package libhwloc-dev:amd64. Preparing to unpack .../087-libhwloc-dev_2.9.0-1_amd64.deb ... Unpacking libhwloc-dev:amd64 (2.9.0-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../088-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../089-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../090-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../091-libxcb1_1.15-1_amd64.deb ... 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Preparing to unpack .../097-libhwloc-plugins_2.9.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.9.0-1) ... Selecting previously unselected package libnl-3-dev:amd64. Preparing to unpack .../098-libnl-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-dev:amd64. Preparing to unpack .../099-libnl-route-3-dev_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs-dev:amd64. Preparing to unpack .../100-libibverbs-dev_44.0-2_amd64.deb ... Unpacking libibverbs-dev:amd64 (44.0-2) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../101-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../102-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../103-libmunge2_0.5.15-2_amd64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../104-libpmix2_4.2.2-1+b1_amd64.deb ... Unpacking libpmix2:amd64 (4.2.2-1+b1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../105-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../106-libopenmpi3_4.1.4-3+b1_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.4-3+b1) ... Selecting previously unselected package openmpi-common. Preparing to unpack .../107-openmpi-common_4.1.4-3_all.deb ... Unpacking openmpi-common (4.1.4-3) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../108-zlib1g-dev_1%3a1.2.13.dfsg-1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... 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Selecting previously unselected package time. Preparing to unpack .../115-time_1.9-0.2_amd64.deb ... Unpacking time (1.9-0.2) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up time (1.9-0.2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libcbor0.8:amd64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:amd64 (1.8.1-1) ... Setting up libgmpxx4ldbl:amd64 (2:6.2.1+dfsg1-1.1) ... Setting up libuv1:amd64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.4-2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libevent-2.1-7:amd64 (2.1.12-stable-8) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:amd64 (1.9.5-4) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libltdl7:amd64 (2.4.7-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up librhash0:amd64 (1.4.3-3) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up chrpath (0.16-2+b1) ... Setting up libsprng2 (2.0a-13) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libgmp-dev:amd64 (2:6.2.1+dfsg1-1.1) ... Setting up libtool (2.4.7-5) ... Setting up libarchive13:amd64 (3.6.2-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libgfortran-12-dev:amd64 (12.2.0-14) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up pkgconf:amd64 (1.8.1-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:amd64 (2.0.16-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:amd64 (2.4.7-5) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up pkg-config:amd64 (1.8.1-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up libnl-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up groff-base (1.22.4-10) ... Setting up libsprng2-dev (2.0a-13) ... Setting up libcurl4:amd64 (7.88.1-8) ... Setting up libx11-6:amd64 (2:1.8.4-2) ... Setting up libhwloc-dev:amd64 (2.9.0-1) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (525.85.05-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.2+b1) ... Setting up cmake (3.25.1-1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up debhelper (13.11.4) ... Setting up libibverbs-dev:amd64 (44.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up libpmix-dev:amd64 (4.2.2-1+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.14) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/446769/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/446769/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+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 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iqtree-2.0.7+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-2.0.7+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/iqtree-2.0.7+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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") 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 "1.2.13") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/iqtree-2.0.7+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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") 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 "1.2.13") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/iqtree-2.0.7+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_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") 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 "1.2.13") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/iqtree-2.0.7+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/terraphast /build/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/ncl /build/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/sprng /build/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/gsl /build/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/booster /build/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/nclextra /build/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/whtest /build/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build [ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build [ 1%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o [ 2%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build [ 3%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o [ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o [ 4%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 6%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 6%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c [ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o [ 7%] Linking CXX static library libvectorclass.a cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 7%] Built target vectorclass make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= [ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 8%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o [ 8%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c [ 8%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 11%] Linking C static library libsprng.a cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 [ 12%] Building C object booster/CMakeFiles/booster.dir/sort.c.o /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 cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 12%] Built target sprng [ 13%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 13%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 13%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 14%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c [ 15%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 16%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 16%] Linking CXX static library libgsl.a cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 16%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c [ 16%] Built target gsl [ 17%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c [ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 17%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_function.h:1438: /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 19%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o /build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 19%] Linking CXX static library liblbfgsb.a In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.omp' [ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o [ 19%] Built target lbfgsb cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 19%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp [ 19%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 21%] Linking C static library libpllavx.a cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.omp' [ 21%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/utils /build/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 21%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 25%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c /build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c [ 28%] Linking CXX static library libwhtest.a cd /build/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 28%] Built target whtest [ 28%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 29%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 29%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 31%] Linking C static library libbooster.a cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 31%] Built target booster [ 31%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c [ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 32%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 32%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 32%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 40%] Linking CXX static library libnclextra.a cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 [ 40%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 40%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c /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-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/pda /build/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 40%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c [ 41%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c [ 42%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c [ 43%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 43%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 43%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c [ 44%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c [ 45%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp [ 47%] Linking CXX static library libterraphast.a cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 48%] Built target terraphast [ 48%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 49%] Linking C static library libpll.a cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 49%] Built target pll [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 52%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 61%] Linking CXX static library libncl.a cd /build/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 61%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/alignment /build/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Linking CXX static library libutils.a cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.omp' [ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/model /build/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 68%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 72%] Linking CXX static library libpda.a cd /build/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 73%] Built target pda make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/main /build/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 74%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Linking CXX static library libphyloYAML.a cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 76%] Built target phyloYAML [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 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-2.0.7+dfsg/build.omp' [ 84%] Built target kernelsse [ 85%] 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-2.0.7+dfsg/build.omp' [ 85%] Built target kernelfma [ 85%] 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-2.0.7+dfsg/build.omp' [ 85%] Built target kernelavx [ 86%] Linking CXX static library libmain.a cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 86%] Built target main [ 86%] Linking CXX static library libalignment.a cd /build/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 86%] Built target alignment [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.omp' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/tree /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/tree /build/iqtree-2.0.7+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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/phylosupertreeunlinked.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 CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terrace /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/terrace /build/iqtree-2.0.7+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+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/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-2.0.7+dfsg/lib: booster/libbooster.a 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 yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/terraphast 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sprng/CMakeFiles/sprng.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/sprng /build/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp [ 0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/gsl /build/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o [ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 4%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 7%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 8%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c [ 10%] Linking C static library libsprng.a cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/iqtree-2.0.7+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 /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_function.h:1438: /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 10%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c [ 10%] Built target sprng make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/booster /build/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c [ 13%] Linking CXX static library libgsl.a cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 14%] Built target gsl make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= [ 14%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 15%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 15%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c [ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 16%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c [ 17%] Linking CXX static library libvectorclass.a cd /build/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 17%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c [ 17%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/nclextra /build/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 22%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 22%] Linking CXX static library liblbfgsb.a cd /build/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.serial' [ 22%] Built target lbfgsb make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/whtest /build/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 22%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 23%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 23%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp [ 23%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 25%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 26%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 26%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp [ 28%] Linking C static library libbooster.a cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o [ 28%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c /usr/bin/ranlib libbooster.a [ 29%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 30%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c [ 30%] Built target booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= [ 30%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 30%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 30%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c [ 31%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c [ 32%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c [ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 33%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c [ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 34%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 34%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c [ 34%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 35%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 38%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] Linking C static library libpll.a cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.serial' [ 40%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 40%] Built target pll make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 41%] Linking C static library libpllavx.a cd /build/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.serial' [ 41%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/utils /build/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 42%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 46%] Linking CXX static library libwhtest.a cd /build/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.serial' [ 46%] Built target whtest [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o [ 49%] Linking CXX static library libnclextra.a cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 49%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/pda /build/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] Linking CXX static library libterraphast.a cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o [ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp /usr/bin/ranlib libterraphast.a [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 54%] Built target terraphast [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 54%] Linking CXX static library libncl.a cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 54%] Built target ncl [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/alignment /build/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= [ 59%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 59%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a [ 65%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 65%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 65%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] Linking CXX static library libutils.a cd /build/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.serial' [ 69%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/model /build/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 72%] Linking CXX static library libpda.a cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 72%] Built target pda make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/main /build/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake --color= /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 73%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 75%] Linking CXX static library libphyloYAML.a cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 75%] Built target phyloYAML [ 75%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 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-2.0.7+dfsg/build.serial' [ 84%] Built target kernelsse [ 85%] 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-2.0.7+dfsg/build.serial' [ 85%] Built target kernelfma [ 85%] 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-2.0.7+dfsg/build.serial' [ 85%] Built target kernelavx [ 85%] Linking CXX static library libalignment.a cd /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd 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CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 86%] Built target main [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 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Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/tree /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/tree /build/iqtree-2.0.7+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 98%] Linking CXX static library libtree.a cd /build/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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/phylosupertreeunlinked.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 CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terrace /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/terrace /build/iqtree-2.0.7+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+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/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-2.0.7+dfsg/lib: booster/libbooster.a 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 yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terraphast /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/ncl /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/ncl /build/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/sprng /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/sprng /build/iqtree-2.0.7+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/gsl /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/gsl /build/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-2.0.7+dfsg/pll/alignment.c cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build [ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 3%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 3%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign' 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro 'rax_posix_memalign' 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro 'rax_posix_memalign' 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro 'rax_posix_memalign' 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro 'rax_posix_memalign' 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-2.0.7+dfsg/sprng/memory.c [ 6%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-2.0.7+dfsg/sprng/store.c [ 7%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-2.0.7+dfsg/pll/hardware.c /build/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu': /build/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro 'rax_posix_memalign' 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro 'rax_posix_memalign' 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 8%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 9%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-2.0.7+dfsg/pll/hash.c [ 9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-2.0.7+dfsg/sprng/checkid.c [ 9%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-2.0.7+dfsg/pll/lexer.c [ 10%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 10%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-2.0.7+dfsg/pll/models.c [ 11%] Linking C static library libsprng.a cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 11%] Built target sprng make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend [ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/booster /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/booster /build/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro 'rax_posix_memalign' 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign' 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-2.0.7+dfsg/booster/bitset_index.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 14%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o [ 14%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashmap.c cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-2.0.7+dfsg/pll/newick.c [ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 15%] Linking CXX static library libgsl.a cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 15%] Built target gsl make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 16%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-2.0.7+dfsg/booster/io.c [ 17%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 18%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-2.0.7+dfsg/booster/sort.c [ 18%] Linking CXX static library libvectorclass.a cd /build/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 18%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/nclextra /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= [ 18%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree.c make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro 'rax_posix_memalign' 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro 'rax_posix_memalign' 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ [ 19%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro 'rax_posix_memalign' 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro 'rax_posix_memalign' 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)': /build/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1781 | cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_function.h:1438: /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylokernel.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-2.0.7+dfsg/pll/queue.c [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 22%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 23%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-2.0.7+dfsg/booster/booster.c [ 23%] Linking CXX static library liblbfgsb.a cd /build/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 23%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-2.0.7+dfsg/pll/recom.c [ 23%] Built target lbfgsb /build/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster': /build/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ /build/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/whtest /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/whtest /build/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 23%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen.c In file included from /build/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 25%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 25%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-2.0.7+dfsg/pll/ssort.c [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 26%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-2.0.7+dfsg/booster/prng.c [ 27%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-2.0.7+dfsg/pll/stack.c [ 27%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-2.0.7+dfsg/pll/topologies.c [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 28%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 29%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-2.0.7+dfsg/booster/stats.c In file included from /build/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-2.0.7+dfsg/pll/treeIO.c [ 31%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-2.0.7+dfsg/whtest/eigen_sym.c In file included from /build/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-2.0.7+dfsg/pll/utils.c [ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp [ 31%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:16: /build/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData': /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro 'rax_posix_memalign' 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro 'rax_posix_memalign' 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro 'rax_posix_memalign' 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro 'rax_posix_memalign' 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro 'rax_posix_memalign' 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro 'rax_posix_memalign' 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro 'rax_posix_memalign' 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro 'rax_posix_memalign' 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro 'rax_posix_memalign' 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro 'rax_posix_memalign' 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign' 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 31%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-2.0.7+dfsg/whtest/random.c [ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 32%] Linking C static library libbooster.a cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 32%] Built target booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pll /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 32%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 33%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest.c In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23, from /build/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 37%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c In file included from /build/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData': /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 39%] Linking C static library libpll.a cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 39%] Built target pll make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 39%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11, from /build/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24, from /build/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 44%] Linking C static library libpllavx.a cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 44%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/utils /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/utils /build/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 44%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 45%] Linking CXX static library libnclextra.a cd /build/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 45%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/pda /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/pda /build/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 46%] Linking CXX static library libwhtest.a cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake [ 46%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/greedy.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] Built target whtest [ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/gzstream.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 47%] Linking CXX static library libterraphast.a cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23, from /build/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 47%] Built target terraphast [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/tools.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.h:23, from /build/iqtree-2.0.7+dfsg/pda/greedy.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/tools.cpp:25: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:18: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/utils/optimization.cpp:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/stoprule.h:23, from /build/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:18, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/map:60, from /build/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Linking CXX static library libncl.a cd /build/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 54%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/alignment /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/alignment /build/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25, from /build/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.h:23, from /build/iqtree-2.0.7+dfsg/pda/pruning.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/split.cpp [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/split.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/graph.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/pda/split.h:27, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:26, from /build/iqtree-2.0.7+dfsg/pda/splitset.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopd.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] Linking CXX static library libutils.a cd /build/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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-2.0.7+dfsg/build.mpi' [ 66%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/model /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/model /build/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 66%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11, from /build/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/utils/optimization.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 68%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modeldna.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21, from /build/iqtree-2.0.7+dfsg/alignment/pattern.h:15, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:17, from /build/iqtree-2.0.7+dfsg/alignment/superalignment.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23, from /build/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.h:23, from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:16, from /build/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /build/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 72%] Linking CXX static library libpda.a cd /build/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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 In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /usr/bin/ranlib libpda.a /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 72%] Built target pda make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/main /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/main /build/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12, from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 73%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-2.0.7+dfsg/main/main.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategamma.cpp /build/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o In file included from /build/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/main.cpp:37: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rategamma.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Linking CXX static library libphyloYAML.a cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 76%] Built target phyloYAML [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/rateinvar.h:23, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11, from /build/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:23, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /usr/include/eigen3/Eigen/Core:50, from /usr/include/eigen3/Eigen/Dense:1, from /build/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-2.0.7+dfsg/main/treetesting.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-2.0.7+dfsg/main/timetree.cpp /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/utils/tools.h:44, from /build/iqtree-2.0.7+dfsg/main/treetesting.h:11, from /build/iqtree-2.0.7+dfsg/main/treetesting.cpp:15: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/main/timetree.h:11, from /build/iqtree-2.0.7+dfsg/main/timetree.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': /build/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 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-2.0.7+dfsg/build.mpi' [ 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-2.0.7+dfsg/build.mpi' [ 84%] Built target kernelavx [ 85%] Linking CXX static library libkernelfma.a 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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-2.0.7+dfsg/build.mpi' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/tree /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/tree /build/iqtree-2.0.7+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/memslot.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/node.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/matree.h:24, from /build/iqtree-2.0.7+dfsg/tree/matree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/node.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.h:23, from /build/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.h:23, from /build/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11, from /build/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.h:23, from /build/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/memslot.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/supernode.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/phylonode.h:15, from /build/iqtree-2.0.7+dfsg/tree/supernode.h:23, from /build/iqtree-2.0.7+dfsg/tree/supernode.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/quartet.cpp:12: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/tinatree.h:23, from /build/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-2.0.7+dfsg/tree/discordance.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/parstree.h:11, from /build/iqtree-2.0.7+dfsg/tree/parstree.cpp:9: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /build/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:29, from /build/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23, from /build/iqtree-2.0.7+dfsg/tree/discordance.cpp:8: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_tree.h:65, from /usr/include/c++/12/set:60, from /build/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 98%] Linking CXX static library libtree.a cd /build/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+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/phylosupertreeunlinked.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 CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/terrace /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/terrace /build/iqtree-2.0.7+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/terrace/terrace.h:27, from /build/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-2.0.7+dfsg -I/build/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp In file included from /build/iqtree-2.0.7+dfsg/ncl/ncl.h:91, from /build/iqtree-2.0.7+dfsg/tree/node.h:37, from /build/iqtree-2.0.7+dfsg/tree/mtree.h:23, from /build/iqtree-2.0.7+dfsg/tree/phylotree.h:36, from /build/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21: /build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, from /build/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+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/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-2.0.7+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a 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 yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.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 yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iqtree-2.0.7+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-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ... + /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 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-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy Seed: 768452 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Apr 25 17:00:57 2023 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)... 0.005 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11226.831 Optimal log-likelihood: -11226.655 Rate parameters: A-C: 1.43107 A-G: 2.31738 A-T: 1.73683 C-G: 1.90653 C-T: 2.79438 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.515 Parameters optimization took 1 rounds (0.073 sec) Time for fast ML tree search: 0.687 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11793.013 93 23772.026 23832.315 24139.435 2 GTR+F+I 11550.829 94 23289.659 23351.458 23661.019 3 GTR+F+G4 11242.079 94 22672.159 22733.958 23043.519 4 GTR+F+I+G4 11226.661 95 22643.323 22706.656 23018.634 5 GTR+F+R2 11338.371 95 22866.742 22930.076 23242.053 6 GTR+F+R3 11227.731 97 22649.462 22715.938 23032.675 7 GTR+F+R4 11220.639 99 22639.278 22708.997 23030.392 8 GTR+F+R5 11220.471 101 22642.943 22716.007 23041.958 17 SYM+I+G4 11229.747 92 22643.495 22702.299 23006.954 30 TVM+F+I+G4 11229.297 94 22646.593 22708.393 23017.954 43 TVMe+I+G4 11231.723 91 22645.446 22702.788 23004.954 56 TIM3+F+I+G4 11240.126 93 22666.252 22726.541 23033.661 69 TIM3e+I+G4 11243.927 90 22667.855 22723.759 23023.412 82 TIM2+F+I+G4 11243.512 93 22673.024 22733.314 23040.434 95 TIM2e+I+G4 11251.105 90 22682.209 22738.114 23037.767 108 TIM+F+I+G4 11231.522 93 22649.043 22709.333 23016.453 121 TIMe+I+G4 11238.215 90 22656.431 22712.335 23011.989 134 TPM3u+F+I+G4 11242.898 92 22669.795 22728.599 23033.254 147 TPM3+F+I+G4 11242.898 92 22669.795 22728.599 23033.254 160 TPM2u+F+I+G4 11246.207 92 22676.414 22735.218 23039.873 173 TPM2+F+I+G4 11246.207 92 22676.414 22735.218 23039.873 186 K3Pu+F+I+G4 11234.112 92 22652.223 22711.027 23015.682 199 K3P+I+G4 11240.039 89 22658.077 22712.567 23009.684 212 TN+F+I+G4 11243.591 92 22671.182 22729.986 23034.641 225 TNe+I+G4 11251.122 89 22680.243 22734.733 23031.850 238 HKY+F+I+G4 11246.299 91 22674.598 22731.941 23034.107 251 K2P+I+G4 11253.033 88 22682.065 22735.163 23029.722 264 F81+F+I+G4 11295.168 90 22770.336 22826.241 23125.894 277 JC+I+G4 11299.159 87 22772.319 22824.048 23116.025 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 5.538 seconds (0h:0m:5s) Wall-clock time for ModelFinder: 5.562 seconds (0h:0m:5s) 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, 1.555 / Estimate: 0.000, 0.956 / LogL: -11246.171 Init pinv, alpha: 0.012, 1.555 / Estimate: 0.083, 1.547 / LogL: -11231.718 Init pinv, alpha: 0.023, 1.555 / Estimate: 0.083, 1.544 / LogL: -11231.720 Init pinv, alpha: 0.035, 1.555 / Estimate: 0.083, 1.542 / LogL: -11231.722 Init pinv, alpha: 0.046, 1.555 / Estimate: 0.083, 1.546 / LogL: -11231.720 Init pinv, alpha: 0.058, 1.555 / Estimate: 0.083, 1.543 / LogL: -11231.725 Init pinv, alpha: 0.069, 1.555 / Estimate: 0.083, 1.540 / LogL: -11231.728 Init pinv, alpha: 0.081, 1.555 / Estimate: 0.083, 1.546 / LogL: -11231.723 Init pinv, alpha: 0.093, 1.555 / Estimate: 0.085, 1.558 / LogL: -11231.721 Init pinv, alpha: 0.104, 1.555 / Estimate: 0.085, 1.564 / LogL: -11231.729 Optimal pinv,alpha: 0.083, 1.547 / LogL: -11231.718 Parameters optimization took 1.972 sec Computing ML distances based on estimated model parameters... 0.052 sec Computing BIONJ tree... 0.002 seconds Log-likelihood of BIONJ tree: -11270.883 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.811 second Computing log-likelihood of 98 initial trees ... 1.375 seconds Current best score: -11231.718 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11231.655 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.144 Iteration 10 / LogL: -11231.227 / Time: 0h:0m:7s Iteration 20 / LogL: -11244.731 / Time: 0h:0m:9s Finish initializing candidate tree set (17) Current best tree score: -11225.144 / CPU time: 7.834 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11225.625 / Time: 0h:0m:12s (0h:0m:31s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 38: -11224.096 Iteration 40 / LogL: -11224.145 / Time: 0h:0m:15s (0h:0m:39s left) BETTER TREE FOUND at iteration 41: -11224.086 Iteration 50 / LogL: -11225.452 / Time: 0h:0m:19s (0h:0m:36s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 52: -11222.902 Iteration 60 / LogL: -11224.433 / Time: 0h:0m:22s (0h:0m:35s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 61: -11222.780 Iteration 70 / LogL: -11224.462 / Time: 0h:0m:25s (0h:0m:33s left) Iteration 80 / LogL: -11224.146 / Time: 0h:0m:27s (0h:0m:28s left) Iteration 90 / LogL: -11222.962 / Time: 0h:0m:30s (0h:0m:23s left) Iteration 100 / LogL: -11241.216 / Time: 0h:0m:32s (0h:0m:19s left) Iteration 110 / LogL: -11222.800 / Time: 0h:0m:34s (0h:0m:16s left) Iteration 120 / LogL: -11223.099 / Time: 0h:0m:37s (0h:0m:12s left) Iteration 130 / LogL: -11222.831 / Time: 0h:0m:40s (0h:0m:9s left) Iteration 140 / LogL: -11231.750 / Time: 0h:0m:42s (0h:0m:6s left) Iteration 150 / LogL: -11222.790 / Time: 0h:0m:45s (0h:0m:3s left) Iteration 160 / LogL: -11227.300 / Time: 0h:0m:47s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 162 ITERATIONS / Time: 0h:0m:48s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.780 Optimal log-likelihood: -11222.778 Rate parameters: A-C: 1.53470 A-G: 2.63887 A-T: 1.69662 C-G: 2.00946 C-T: 2.63887 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: 1.530 Parameters optimization took 1 rounds (0.046 sec) BEST SCORE FOUND : -11222.778 Total tree length: 12.601 Total number of iterations: 162 CPU time used for tree search: 45.247 sec (0h:0m:45s) Wall-clock time used for tree search: 46.369 sec (0h:0m:46s) Total CPU time used: 47.389 sec (0h:0m:47s) Total wall-clock time used: 48.520 sec (0h:0m:48s) 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: Tue Apr 25 17:01:51 2023 real 0m54.094s user 0m52.928s sys 0m0.683s + /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 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-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo Seed: 862906 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Tue Apr 25 17:01:51 2023 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)... 0.006 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11239.760 Optimal log-likelihood: -11239.649 Rate parameters: A-C: 1.45046 A-G: 2.32044 A-T: 1.74141 C-G: 1.90741 C-T: 2.78602 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.549 Parameters optimization took 1 rounds (0.048 sec) Time for fast ML tree search: 0.528 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11797.808 93 23781.615 23841.905 24149.025 2 GTR+F+I 11556.535 94 23301.070 23362.869 23672.430 3 GTR+F+G4 11255.917 94 22699.833 22761.633 23071.194 4 GTR+F+I+G4 11239.658 95 22669.316 22732.649 23044.627 5 GTR+F+R2 11346.095 95 22882.189 22945.522 23257.500 6 GTR+F+R3 11241.184 97 22676.368 22742.843 23059.580 7 GTR+F+R4 11233.752 99 22665.504 22735.223 23056.618 8 GTR+F+R5 11233.332 101 22668.665 22741.728 23067.680 17 SYM+I+G4 11242.729 92 22669.457 22728.261 23032.916 30 TVM+F+I+G4 11242.143 94 22672.286 22734.085 23043.646 43 TVMe+I+G4 11244.615 91 22671.230 22728.573 23030.739 56 TIM3+F+I+G4 11253.755 93 22693.511 22753.800 23060.920 69 TIM3e+I+G4 11257.581 90 22695.161 22751.066 23050.719 82 TIM2+F+I+G4 11257.451 93 22700.903 22761.192 23068.312 95 TIM2e+I+G4 11265.345 90 22710.689 22766.594 23066.247 108 TIM+F+I+G4 11245.392 93 22676.783 22737.073 23044.193 121 TIMe+I+G4 11252.268 90 22684.536 22740.441 23040.094 134 TPM3u+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 147 TPM3+F+I+G4 11256.410 92 22696.820 22755.625 23060.280 160 TPM2u+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 173 TPM2+F+I+G4 11260.016 92 22704.032 22762.836 23067.491 186 K3Pu+F+I+G4 11247.847 92 22679.694 22738.498 23043.153 199 K3P+I+G4 11254.005 89 22686.010 22740.500 23037.617 212 TN+F+I+G4 11257.649 92 22699.298 22758.102 23062.757 225 TNe+I+G4 11265.431 89 22708.861 22763.351 23060.468 238 HKY+F+I+G4 11260.239 91 22702.477 22759.820 23061.986 251 K2P+I+G4 11267.270 88 22710.539 22763.638 23058.196 264 F81+F+I+G4 11308.833 90 22797.666 22853.571 23153.224 277 JC+I+G4 11313.164 87 22800.329 22852.059 23144.035 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 5.411 seconds (0h:0m:5s) Wall-clock time for ModelFinder: 5.480 seconds (0h:0m:5s) 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, 1.590 / Estimate: 0.000, 0.970 / LogL: -11259.840 Init pinv, alpha: 0.012, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.628 Init pinv, alpha: 0.023, 1.590 / Estimate: 0.084, 1.581 / LogL: -11244.611 Init pinv, alpha: 0.035, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.613 Init pinv, alpha: 0.046, 1.590 / Estimate: 0.084, 1.582 / LogL: -11244.612 Init pinv, alpha: 0.058, 1.590 / Estimate: 0.084, 1.579 / LogL: -11244.618 Init pinv, alpha: 0.069, 1.590 / Estimate: 0.084, 1.576 / LogL: -11244.620 Init pinv, alpha: 0.081, 1.590 / Estimate: 0.084, 1.580 / LogL: -11244.615 Init pinv, alpha: 0.093, 1.590 / Estimate: 0.085, 1.592 / LogL: -11244.613 Init pinv, alpha: 0.104, 1.590 / Estimate: 0.086, 1.598 / LogL: -11244.621 Optimal pinv,alpha: 0.084, 1.581 / LogL: -11244.611 Parameters optimization took 1.812 sec Computing ML distances based on estimated model parameters... 0.046 sec Computing BIONJ tree... 0.002 seconds Log-likelihood of BIONJ tree: -11270.724 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.706 second Computing log-likelihood of 98 initial trees ... 1.267 seconds Current best score: -11244.611 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11244.583 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -11225.129 Iteration 10 / LogL: -11232.240 / Time: 0h:0m:5s Iteration 20 / LogL: -11231.938 / Time: 0h:0m:8s Finish initializing candidate tree set (14) Current best tree score: -11225.129 / CPU time: 6.229 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11225.347 / Time: 0h:0m:11s (0h:0m:27s left) Iteration 40 / LogL: -11237.948 / Time: 0h:0m:13s (0h:0m:21s left) UPDATE BEST LOG-LIKELIHOOD: -11225.129 Iteration 50 / LogL: -11225.279 / Time: 0h:0m:16s (0h:0m:17s left) Iteration 60 / LogL: -11231.806 / Time: 0h:0m:19s (0h:0m:13s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 64: -11222.898 Iteration 70 / LogL: -11225.249 / Time: 0h:0m:22s (0h:0m:30s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 80: -11222.776 Iteration 80 / LogL: -11222.776 / Time: 0h:0m:25s (0h:0m:32s left) Iteration 90 / LogL: -11224.114 / Time: 0h:0m:30s (0h:0m:30s left) Iteration 100 / LogL: -11222.925 / Time: 0h:0m:33s (0h:0m:26s left) Iteration 110 / LogL: -11226.476 / Time: 0h:0m:35s (0h:0m:22s left) Iteration 120 / LogL: -11222.927 / Time: 0h:0m:38s (0h:0m:19s left) Iteration 130 / LogL: -11222.795 / Time: 0h:0m:40s (0h:0m:15s left) Iteration 140 / LogL: -11223.317 / Time: 0h:0m:44s (0h:0m:12s left) Iteration 150 / LogL: -11223.131 / Time: 0h:0m:47s (0h:0m:9s left) Iteration 160 / LogL: -11223.097 / Time: 0h:0m:49s (0h:0m:6s left) UPDATE BEST LOG-LIKELIHOOD: -11222.775 Iteration 170 / LogL: -11223.153 / Time: 0h:0m:52s (0h:0m:3s left) Iteration 180 / LogL: -11226.283 / Time: 0h:0m:55s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 181 ITERATIONS / Time: 0h:0m:55s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.775 Optimal log-likelihood: -11222.772 Rate parameters: A-C: 1.51825 A-G: 2.61371 A-T: 1.67570 C-G: 1.98422 C-T: 2.61371 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: 1.530 Parameters optimization took 1 rounds (0.045 sec) BEST SCORE FOUND : -11222.772 Total tree length: 12.605 Total number of iterations: 181 CPU time used for tree search: 50.942 sec (0h:0m:50s) Wall-clock time used for tree search: 53.823 sec (0h:0m:53s) Total CPU time used: 52.923 sec (0h:0m:52s) Total wall-clock time used: 55.804 sec (0h:0m:55s) 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: Tue Apr 25 17:02:53 2023 real 1m1.299s user 0m58.337s sys 0m0.644s + rm -rf /tmp/iqtree-test.wnqM2S 111.29user 1.35system 1:55.44elapsed 97%CPU (0avgtext+0avgdata 15732maxresident)k 0inputs+0outputs (0major+6631minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j15 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 -- Set runtime path of "/build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j15 install DESTDIR=/build/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-2.0.7+dfsg -B/build/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi -- Set runtime path of "/build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' dh_install find debian -name iqtree2-mpi -exec chrpath --delete \{\} \; find debian -name iqtree2-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/iqtree-2.0.7+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-2.0.7+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/iqtree-2.0.7+dfsg' mkdir -p /build/iqtree-2.0.7+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="2.0.7+dfsg" /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/build/iqtree-2.0.7+dfsg' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../iqtree_2.0.7+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) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/446769/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/446769/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/446769 and its subdirectories I: Current time: Tue Apr 25 17:04:59 +14 2023 I: pbuilder-time-stamp: 1682391899