Tue Apr 25 01:58:36 UTC 2023 I: starting to build iqtree/bookworm/amd64 on jenkins on '2023-04-25 01:58'
Tue Apr 25 01:58:36 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_12/32101/console.log
Tue Apr 25 01:58:36 UTC 2023 I: Downloading source for bookworm/iqtree=2.0.7+dfsg-1
--2023-04-25 01:58:37-- http://cdn-fastly.deb.debian.org/debian/pool/main/i/iqtree/iqtree_2.0.7%2bdfsg-1.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
Length: 2236 (2.2K) [text/prs.lines.tag]
Saving to: ‘iqtree_2.0.7+dfsg-1.dsc’
0K .. 100% 178M=0s
2023-04-25 01:58:37 (178 MB/s) - ‘iqtree_2.0.7+dfsg-1.dsc’ saved [2236/2236]
Tue Apr 25 01:58:37 UTC 2023 I: iqtree_2.0.7+dfsg-1.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: iqtree
Binary: iqtree
Architecture: amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386
Version: 2.0.7+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Kevin Murray <kdmfoss@gmail.com>
Homepage: http://www.cibiv.at/software/iqtree/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/iqtree
Vcs-Git: https://salsa.debian.org/med-team/iqtree.git
Testsuite: autopkgtest
Testsuite-Triggers: time
Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath
Package-List:
iqtree deb science optional arch=amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386
Checksums-Sha1:
55d95bdac2da0ae814d1823a6e3fdd40cc41fe83 1581628 iqtree_2.0.7+dfsg.orig.tar.xz
f80d1bef58520f5fc6bafa50347d04056671a579 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz
Checksums-Sha256:
95a3a9c3b32aeb8caa63307808fed7fad68f20f877f3fe5fe751af1d49cbdb86 1581628 iqtree_2.0.7+dfsg.orig.tar.xz
704055ba4585527dacedf6b6cdf5d796c4fd20828fcd48c4d6856601b422e9d6 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz
Files:
1c1bbda0de4ede3114cd8f7c67128cac 1581628 iqtree_2.0.7+dfsg.orig.tar.xz
c48f5516b5986759881c990fffc68664 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=Pwr1
-----END PGP SIGNATURE-----
Tue Apr 25 01:58:37 UTC 2023 I: Checking whether the package is not for us
Tue Apr 25 01:58:37 UTC 2023 I: Starting 1st build on remote node ionos15-amd64.debian.net.
Tue Apr 25 01:58:37 UTC 2023 I: Preparing to do remote build '1' on ionos15-amd64.debian.net.
Tue Apr 25 02:42:55 UTC 2023 I: Deleting $TMPDIR on ionos15-amd64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Sun May 26 20:21:41 -12 2024
I: pbuilder-time-stamp: 1716798101
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 Fri Jan 21 02:08:08 2022 -12
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/2789017/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='amd64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16'
DISTRIBUTION='bookworm'
HOME='/root'
HOST_ARCH='amd64'
IFS='
'
INVOCATION_ID='4477be8833ac4b5caec5400176e1422d'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='2789017'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/pbuilderrc_efrB --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b1 --logfile b1/build.log iqtree_2.0.7+dfsg-1.dsc'
SUDO_GID='111'
SUDO_UID='106'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://85.184.249.68:3128'
I: uname -a
Linux ionos15-amd64 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux
I: ls -l /bin
total 5632
-rwxr-xr-x 1 root root 1265648 Feb 12 2023 bash
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep
-rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2
-rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore
-rwxr-xr-x 1 root root 44016 Sep 20 2022 cat
-rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp
-rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod
-rwxr-xr-x 1 root root 72752 Sep 20 2022 chown
-rwxr-xr-x 1 root root 151152 Sep 20 2022 cp
-rwxr-xr-x 1 root root 125640 Jan 5 2023 dash
-rwxr-xr-x 1 root root 121904 Sep 20 2022 date
-rwxr-xr-x 1 root root 89240 Sep 20 2022 dd
-rwxr-xr-x 1 root root 102200 Sep 20 2022 df
-rwxr-xr-x 1 root root 151344 Sep 20 2022 dir
-rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname
-rwxr-xr-x 1 root root 43856 Sep 20 2022 echo
-rwxr-xr-x 1 root root 41 Jan 24 2023 egrep
-rwxr-xr-x 1 root root 35664 Sep 20 2022 false
-rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep
-rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt
-rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount
-rwxr-xr-x 1 root root 203152 Jan 24 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe
-rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip
-rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname
-rwxr-xr-x 1 root root 72824 Sep 20 2022 ln
-rwxr-xr-x 1 root root 53024 Mar 23 2023 login
-rwxr-xr-x 1 root root 151344 Sep 20 2022 ls
-rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk
-rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir
-rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod
-rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp
-rwxr-xr-x 1 root root 59712 Mar 22 2023 more
-rwsr-xr-x 1 root root 59704 Mar 22 2023 mount
-rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint
-rwxr-xr-x 1 root root 142968 Sep 20 2022 mv
lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd
lrwxrwxrwx 1 root root 4 Feb 12 2023 rbash -> bash
-rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink
-rwxr-xr-x 1 root root 72752 Sep 20 2022 rm
-rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir
-rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts
-rwxr-xr-x 1 root root 126424 Jan 5 2023 sed
lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash
-rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep
-rwxr-xr-x 1 root root 85008 Sep 20 2022 stty
-rwsr-xr-x 1 root root 72000 Mar 22 2023 su
-rwxr-xr-x 1 root root 39824 Sep 20 2022 sync
-rwxr-xr-x 1 root root 531984 Apr 6 2023 tar
-rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile
-rwxr-xr-x 1 root root 109616 Sep 20 2022 touch
-rwxr-xr-x 1 root root 35664 Sep 20 2022 true
-rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server
-rwsr-xr-x 1 root root 35128 Mar 22 2023 umount
-rwxr-xr-x 1 root root 43888 Sep 20 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress
-rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir
-rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 9 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 9 2022 znew
I: user script /srv/workspace/pbuilder/2789017/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 <pbuilder-maint@lists.alioth.debian.org>
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 2s (37.6 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 ...
Unpacking libxcb1:amd64 (1.15-1) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../092-libx11-data_2%3a1.8.4-2_all.deb ...
Unpacking libx11-data (2:1.8.4-2) ...
Selecting previously unselected package libx11-6:amd64.
Preparing to unpack .../093-libx11-6_2%3a1.8.4-2_amd64.deb ...
Unpacking libx11-6:amd64 (2:1.8.4-2) ...
Selecting previously unselected package libxext6:amd64.
Preparing to unpack .../094-libxext6_2%3a1.3.4-1+b1_amd64.deb ...
Unpacking libxext6:amd64 (2:1.3.4-1+b1) ...
Selecting previously unselected package libxnvctrl0:amd64.
Preparing to unpack .../095-libxnvctrl0_525.85.05-1_amd64.deb ...
Unpacking libxnvctrl0:amd64 (525.85.05-1) ...
Selecting previously unselected package ocl-icd-libopencl1:amd64.
Preparing to unpack .../096-ocl-icd-libopencl1_2.3.1-1_amd64.deb ...
Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ...
Selecting previously unselected package libhwloc-plugins:amd64.
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) ...
Selecting previously unselected package libpmix-dev:amd64.
Preparing to unpack .../109-libpmix-dev_4.2.2-1+b1_amd64.deb ...
Unpacking libpmix-dev:amd64 (4.2.2-1+b1) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../110-openmpi-bin_4.1.4-3+b1_amd64.deb ...
Unpacking openmpi-bin (4.1.4-3+b1) ...
Selecting previously unselected package libopenmpi-dev:amd64.
Preparing to unpack .../111-libopenmpi-dev_4.1.4-3+b1_amd64.deb ...
Unpacking libopenmpi-dev:amd64 (4.1.4-3+b1) ...
Selecting previously unselected package libsprng2.
Preparing to unpack .../112-libsprng2_2.0a-13_amd64.deb ...
Unpacking libsprng2 (2.0a-13) ...
Selecting previously unselected package libsprng2-dev.
Preparing to unpack .../113-libsprng2-dev_2.0a-13_amd64.deb ...
Unpacking libsprng2-dev (2.0a-13) ...
Selecting previously unselected package mpi-default-dev.
Preparing to unpack .../114-mpi-default-dev_1.14_amd64.deb ...
Unpacking mpi-default-dev (1.14) ...
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
I: Building the package
I: Running cd /build/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../iqtree_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 <tille@debian.org>
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 <min> value or use a ...<max> 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 <min> value or use a ...<max> 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 <min> value or use a ...<max> 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 -j16 "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[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 CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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 terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.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 -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
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 -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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/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]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
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 -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
make[4]: Leaving 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
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'
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 -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build
make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
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 -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend
[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.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 -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -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]: Leaving 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 -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 && /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 -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
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'
[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.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
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
[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
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]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build
[ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.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/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.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
[ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
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
[ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
[ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
make[4]: Leaving 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/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
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
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
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
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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
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
make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.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 -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 4%] Building C object sprng/CMakeFiles/sprng.dir/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/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
[ 5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.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/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 lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
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
[ 6%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
[ 7%] 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
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
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));
| ^~~~~~~~~~~~~~~~~~
[ 7%] 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
[ 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
[ 8%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.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/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
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/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);
| ^~~~~~~~~~~~~~~
[ 8%] 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
[ 8%] 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
[ 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
[ 9%] Linking CXX static library libvectorclass.a
cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
cd /build/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1
[ 10%] Building C object sprng/CMakeFiles/sprng.dir/store.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/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
/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'
[ 10%] 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
[ 10%] 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.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=
[ 10%] 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 10%] 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
[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
[ 11%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.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
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
[ 12%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 booster/CMakeFiles/booster.dir/sort.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
[ 13%] 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
[ 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
[ 13%] Building C object sprng/CMakeFiles/sprng.dir/checkid.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/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
[ 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
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);
| ^~~~~~~~~~~~~~~~~~
[ 14%] 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
/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
[ 15%] 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
/usr/bin/ranlib libsprng.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 15%] Built target sprng
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.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/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]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 15%] 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
[ 15%] 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
[ 15%] 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'
[ 15%] Built target gsl
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=
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'
[ 15%] 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
[ 15%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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
[ 16%] 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);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 17%] 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/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);
| ^~~~~~~~~~~~~~~~~~
[ 18%] 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
[ 18%] 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
[ 18%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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/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);
| ^~~~~~~~~~~~~~~
[ 20%] 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
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));
| ^~~~~~~~~~~~~~~~~~
[ 21%] 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
[ 21%] 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
[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.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/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
[ 21%] 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
/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%] 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
[ 22%] 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
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/phylotreeavx.cpp:11:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 22%] 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
[ 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
[ 22%] Linking CXX static library liblbfgsb.a
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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib liblbfgsb.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 22%] Built target lbfgsb
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.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'
[ 22%] 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
[ 23%] 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
[ 24%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 24%] 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
[ 25%] 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
[ 26%] 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
[ 26%] 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
[ 27%] 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
[ 28%] 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
[ 28%] 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
/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 );
| ^~~~~~~~~~~~~~~~~~~~~~~~
[ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.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/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
[ 29%] 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
/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'
[ 29%] 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
[ 29%] Built target booster
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'
[ 29%] 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
[ 30%] 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
[ 30%] 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
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'
[ 31%] 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
[ 31%] Built target pllavx
[ 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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 utils/CMakeFiles/utils.dir/optimization.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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 33%] 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
[ 33%] 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
[ 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
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);
| ^~~~~~~~~~~~~~~
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 34%] 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
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));
| ^~~~~~~~~~~~~~~~~~
[ 35%] 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
[ 35%] 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
[ 36%] 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
[ 36%] 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
[ 36%] 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
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);
| ^~~~~~~~~~~~~~~
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
[ 37%] 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
/usr/bin/ranlib libterraphast.a
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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
/usr/bin/ranlib libwhtest.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 37%] Built target terraphast
[ 37%] Built target whtest
[ 38%] 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
[ 38%] 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
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);
| ^~~~~~~~~~~~~~~
[ 38%] 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
[ 39%] 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
[ 40%] 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
[ 40%] 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
[ 40%] 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/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);
| ^~~~~~~~~~~~~~~
[ 41%] 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
[ 41%] 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
[ 42%] 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/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);
| ^~~~~~~~~~~~~~~
[ 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/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
[ 43%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o
[ 45%] 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/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
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
[ 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/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 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
[ 46%] 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
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);
| ^~~~~~~~~~~~~~~
[ 47%] 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
[ 47%] 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/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);
| ^~~~~~~~~~~~~~~
[ 47%] 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
[ 47%] 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
[ 47%] 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/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) *
| ^~~~~~~~~~~~~~~~~~
[ 47%] 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
[ 48%] 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
[ 48%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 48%] 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
[ 49%] 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
[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.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/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
[ 50%] 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
[ 50%] 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
[ 51%] 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
[ 51%] 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
/usr/bin/ranlib libpll.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 51%] Built target pll
[ 52%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxsdatablock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 53%] 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
[ 53%] 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
[ 54%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 54%] 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
[ 55%] 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
[ 55%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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
/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'
[ 56%] 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'
[ 56%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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
[ 57%] 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
[ 57%] 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
[ 57%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 58%] 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
[ 58%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/ncl/nxsexception.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 59%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 59%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxsstring.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxstaxablock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 60%] 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
[ 60%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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%] 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 62%] 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
[ 63%] 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
[ 63%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 64%] 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"
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib libyaml-cpp.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 64%] Built target yaml-cpp
make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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=
[ 64%] 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
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'
cd /build/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1
[ 64%] 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
/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'
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
[ 64%] Built target utils
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
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
[ 67%] 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
[ 67%] 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
[ 67%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pda/pdtree.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelmarkov.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib libncl.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 67%] Built target ncl
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
[ 68%] 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
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=
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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'
[ 68%] 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
/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/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);
| ^~~~~
/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*);
| ^~~~~
[ 68%] 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
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 69%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 69%] 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
[ 69%] 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
/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) {
| ^~~~~
[ 69%] 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
[ 70%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/rategamma.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 71%] 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
[ 71%] 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
[ 71%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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*);
| ^~~~~
/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/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*);
| ^~~~~
[ 72%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/ratemeyerdiscrete.cpp:21:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/alignmentpairwise.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 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.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'
[ 73%] 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
[ 74%] 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
[ 74%] 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
/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__;
| ^~~~~~~~
[ 75%] 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
[ 75%] 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
[ 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
[ 77%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.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/main/main.cpp:37:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 /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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib libphyloYAML.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 77%] Built target phyloYAML
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelcodon.cpp.o
[ 77%] 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
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/ratekategory.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/ratefree.cpp:8:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelmixture.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/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
[ 78%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelmixture.cpp:8:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
[ 79%] 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*);
| ^~~~~
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);
| ^~~~~
/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: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/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) {
| ^~~~~
[ 79%] 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
[ 79%] 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
[ 80%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 81%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 81%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/superalignment.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 82%] 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/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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
[ 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
[ 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
[ 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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
[ 84%] Linking CXX static library libkernelavx.a
/usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake
[ 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/kernelavx.dir/link.txt --verbose=1
/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
/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 libkernelavx.a
/usr/bin/ranlib libkernelfma.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.omp'
[ 85%] Built target kernelavx
[ 85%] Built target kernelfma
[ 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
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
[ 89%] 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/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/memslot.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
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.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/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
[ 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/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
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.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
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
[ 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/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.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
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.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
[ 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/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
[ 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/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.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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/node.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 /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/phylotree.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 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
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/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*);
| ^~~~~
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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/phylotreesse.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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 | }
| ^
[ 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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/discordance.cpp:8:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 -j16 "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 -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 -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
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.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[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 -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 /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 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/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]: 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=
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/pll.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/terraphast /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/terraphast /build/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.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/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 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/ncl /build/iqtree-2.0.7+dfsg/build.serial /build/iqtree-2.0.7+dfsg/build.serial/ncl /build/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color=
make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
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=
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]: 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 -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
make[4]: Entering 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/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/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[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
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/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build
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]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
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=
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 -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
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]: 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=
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
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
/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/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
make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build
[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
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 -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.serial'
[ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build
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 booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
make[4]: Leaving 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 -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
[ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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/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.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 ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
[ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.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/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
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
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build
[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.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/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 yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build
[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
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
[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
[ 5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.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
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
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.serial'
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
[ 6%] 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
[ 6%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o
[ 6%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
[ 6%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.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
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
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/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));
| ^~~~~~~~~~~~~~~~~~
[ 7%] 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
[ 7%] 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
[ 7%] 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
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'
[ 7%] Built target vectorclass
[ 7%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.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/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
[ 7%] 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
[ 7%] 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
[ 7%] 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 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
[ 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/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);
| ^~~~~~~~~~~~~~~
[ 8%] 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/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 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
[ 10%] 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
[ 10%] 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
[ 10%] 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
[ 11%] 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
[ 11%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.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
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/nxsassumptionsblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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
cd /build/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1
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);
| ^~~~~~~~~~~~~~~
/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.serial'
[ 12%] Built target sprng
[ 12%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 14%] 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
[ 14%] 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 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
cd /build/iqtree-2.0.7+dfsg/build.serial/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
/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);
| ^~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 15%] 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
[ 15%] Built target gsl
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);
| ^~~~~~~~~~~~~~~~~~
[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.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/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
[ 17%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 17%] 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
[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.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
[ 18%] 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
[ 18%] 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
[ 18%] 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
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/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);
| ^~~~~~~~~~~~~~~
[ 19%] 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
[ 19%] 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
[ 20%] 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
[ 20%] 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
[ 20%] 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
/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);
| ~~~~~~^~~~~~~~
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);
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 21%] 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
[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.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/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
[ 21%] 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
[ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
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);
| ^~~~~~~~~~~~~~~
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/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);
| ^~~~~~~~~~~~~~~~~~
[ 21%] 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
/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));
| ^~~~~~~~~~~~~~~~~~
/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
/usr/bin/ranlib liblbfgsb.a
[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
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
[ 22%] Built target lbfgsb
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=
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'
[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o
/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 );
| ^~~~~~~~~~~~~~~~~~~~~~~~
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
[ 22%] 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
[ 23%] 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
[ 24%] 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'
[ 24%] Built target pllavx
[ 24%] 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
[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.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/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
[ 26%] 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
[ 26%] 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
[ 27%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o
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);
| ^~~~~~~~~~~~~~~
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
[ 27%] 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/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);
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.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/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
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
[ 29%] 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
/usr/bin/ranlib libbooster.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 30%] 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
[ 30%] Built target booster
[ 30%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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);
| ^~~~~~~~~~~~~~~
[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 31%] 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
/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)
| ^~~~~~~
[ 32%] 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
[ 32%] 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
[ 33%] 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
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);
| ^~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~
[ 34%] 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/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);
| ^~~~~~~~~~~~~~~
[ 34%] 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
[ 34%] 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
[ 34%] 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
[ 34%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
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);
| ^~~~~~~~~~~~~~~
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
[ 35%] 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
[ 35%] 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
[ 36%] 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/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);
| ^~~~~~~~~~~~~~~
[ 36%] 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
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);
| ^~~~~~~~~~~~~~~
[ 37%] 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
[ 37%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 38%] Linking CXX static library libnclextra.a
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
[ 38%] 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);
| ^~~~~~~~~~~~~~~
/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'
[ 38%] Built target nclextra
[ 38%] 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
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) *
| ^~~~~~~~~~~~~~~~~~
[ 39%] 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
[ 40%] 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
[ 41%] 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 41%] Built target whtest
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'
[ 41%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 41%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 41%] 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/nxsdatablock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 41%] 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
[ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.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
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
[ 43%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 44%] 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
[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.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/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
/usr/bin/ranlib libpll.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 45%] Built target pll
[ 45%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 45%] 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
[ 46%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 46%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pda/gurobiwrapper.cpp:24:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 47%] 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
[ 47%] 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
[ 48%] 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
[ 48%] 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
[ 48%] 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
[ 48%] 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
[ 48%] 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
[ 49%] 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/ncl/nxsdistancedatum.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 50%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 51%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 52%] 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
[ 52%] 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 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
[ 52%] 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/ncl/nxsdistancesblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.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/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
[ 54%] 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
[ 54%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 55%] 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
[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o
[ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.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
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
[ 55%] 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
[ 56%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 57%] 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/nxsexception.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 57%] 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
[ 58%] 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
[ 58%] 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
[ 59%] 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
[ 59%] 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/ncl/nxsstring.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxssetreader.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/ncl/nxstaxablock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 59%] 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/ncl/nxstoken.cpp:19:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 59%] 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
[ 59%] 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
/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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 59%] Built target terraphast
[ 60%] 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/ncl/nxstreesblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 60%] 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
[ 61%] 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
[ 61%] 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
[ 61%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.serial'
[ 61%] 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'
[ 61%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 62%] 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
[ 62%] 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
[ 62%] 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
[ 63%] 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
[ 64%] 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
[ 64%] 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
[ 64%] 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
[ 65%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pda/pdtree.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 66%] Building CXX object model/CMakeFiles/model.dir/modelbin.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
[ 66%] 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
[ 66%] 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
[ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
cd /build/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1
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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
/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 /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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib libncl.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 66%] Built target ncl
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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=
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'
[ 66%] 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
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 66%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pattern.cpp:12:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 67%] 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
/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/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);
| ^~~~~
[ 68%] 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"
[ 69%] 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
/usr/bin/ranlib libyaml-cpp.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 69%] 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'
[ 69%] 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
[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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
[ 70%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 71%] 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
[ 71%] 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
/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*);
| ^~~~~
/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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 72%] 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 73%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 73%] 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
[ 74%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 74%] 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
[ 74%] 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
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/usr/bin/ranlib libpda.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 74%] 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=
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'
[ 75%] 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/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__;
| ^~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
/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
| ^~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 76%] 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
[ 77%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 79%] 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'
[ 79%] Built target phyloYAML
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/rateheterotachy.cpp:9:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
[ 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
[ 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
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelmixture.cpp:8:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
[ 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
[ 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
/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) {
| ^~~~~
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelpomo.cpp:1:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/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/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);
| ^~~~~
/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: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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
[ 86%] Linking CXX static library libmain.a
cd /build/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
cd /build/iqtree-2.0.7+dfsg/build.serial/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.serial'
[ 86%] Built target main
[ 86%] 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 /build/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
/usr/bin/ranlib libalignment.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.serial'
[ 86%] Built target alignment
[ 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 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.serial'
[ 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.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
[ 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/candidateset.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.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
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
[ 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/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
[ 89%] 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/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
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
[ 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/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/ncbitree.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
[ 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/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
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/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/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
[ 94%] 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/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/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/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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/phylotree.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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/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
[ 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
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/quartet.cpp:12:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 -j16 "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 -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 -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
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 -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.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[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 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 /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 pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend
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/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=
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=
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/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]: 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]: 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[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[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[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[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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
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/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]: 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 CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.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'
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
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 CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build
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]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
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[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.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 -g -O2 -ffile-prefix-map=/build/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-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]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.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]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 1%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.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'
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
[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.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.mpi'
[ 1%] Building C object booster/CMakeFiles/booster.dir/hashmap.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
[ 2%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
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'
[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.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
/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
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
make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
[ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
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'
make[4]: Entering 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
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
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
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
[ 3%] Building C object sprng/CMakeFiles/sprng.dir/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/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
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
[ 4%] 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
[ 4%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
[ 5%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
[ 5%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.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
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
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
[ 5%] 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/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);
| ^~~~~~~~~~~~~~~
[ 5%] 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
[ 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
[ 6%] 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
[ 7%] 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
[ 7%] 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
[ 7%] 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
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
[ 8%] 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 8%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
[ 8%] Built target vectorclass
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
[ 9%] 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
/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);
| ~~~~~~^~~~~~~~
[ 10%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.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
[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
[ 12%] Building C object sprng/CMakeFiles/sprng.dir/store.c.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
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
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));
| ^~~~~~~~~~~~~~~~~~
[ 12%] 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
[ 12%] 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
[ 12%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.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/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
[ 12%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
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);
| ^~~~~~~~~~~~~~~
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
[ 12%] 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
[ 12%] 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
[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.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/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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxsassumptionsblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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'
[ 13%] Built target sprng
[ 14%] 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
[ 14%] 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
[ 15%] 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
[ 16%] 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
[ 16%] 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
[ 16%] 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
[ 16%] 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
/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'
[ 16%] Built target gsl
[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.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/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
[ 18%] 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
[ 18%] 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
[ 18%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 19%] 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
[ 20%] 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
/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 );
| ^~~~~~~~~~~~~~~~~~~~~~~~
[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.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/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
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
[ 21%] 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
[ 21%] 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
/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'
[ 21%] Built target booster
[ 21%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.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/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
[ 22%] 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
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);
| ^~~~~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~~~~
[ 23%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/phylokernelfma.cpp:11:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 23%] 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
[ 24%] 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'
[ 24%] Built target pllavx
[ 24%] 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
[ 24%] 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
[ 24%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 25%] 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
[ 26%] 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
[ 26%] 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
[ 26%] 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'
[ 27%] 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
[ 27%] Built target lbfgsb
[ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.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/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
[ 27%] 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
[ 27%] 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
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));
| ^~~~~~~~~~~~~~~~~~
[ 28%] 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/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);
| ^~~~~~~~~~~~~~~
[ 28%] 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
[ 29%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 30%] 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
[ 31%] 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
[ 32%] 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
cd /build/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1
/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
/usr/bin/ranlib libwhtest.a
[ 32%] 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 32%] Built target whtest
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'
[ 32%] 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
[ 32%] 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
[ 32%] 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
[ 33%] 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
[ 34%] 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
[ 34%] Building C object pll/CMakeFiles/pll.dir/newick.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/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);
| ^~~~~~~~~~~~~~~
[ 35%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 35%] 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
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/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)
| ^~~~~~~
/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 36%] 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
[ 36%] 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
[ 36%] 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
[ 37%] 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
[ 37%] 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
[ 37%] 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
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);
| ^~~~~~~~~~~~~~~
[ 38%] 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
[ 38%] 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
[ 38%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 40%] 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
[ 41%] 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
[ 41%] 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
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);
| ^~~~~~~~~~~~~~~
[ 41%] 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
[ 41%] 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
[ 42%] 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
[ 43%] 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
[ 43%] 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
[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o
[ 43%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.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
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
[ 43%] 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);
| ^~~~~~~~~~~~~~~
[ 43%] Building C object pll/CMakeFiles/pll.dir/queue.c.o
[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.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/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
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
[ 44%] 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
[ 45%] 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);
| ^~~~~~~~~~~~~~~
[ 45%] 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
[ 46%] 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
[ 47%] 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/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);
| ^~~~~~~~~~~~~~~
[ 47%] 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
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);
| ^~~~~~~~~~~~~~~
[ 47%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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);
| ^~~~~~~~~~~~~~~
[ 48%] 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
[ 49%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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);
| ^~~~~~~~~~~~~~~
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);
| ^~~~~~~~~~~~~~~
[ 49%] 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
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);
| ^~~~~~~~~~~~~~~
[ 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
[ 49%] 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
[ 49%] 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/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) *
| ^~~~~~~~~~~~~~~~~~
[ 50%] 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
[ 50%] 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
[ 50%] 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
[ 51%] 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
[ 51%] 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
[ 52%] 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'
[ 52%] 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=
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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'
[ 52%] 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
[ 52%] 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
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 52%] Built target terraphast
[ 52%] 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
[ 53%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 53%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 54%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
/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'
[ 54%] Built target pll
[ 54%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxsdiscretematrix.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 55%] 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
[ 55%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 56%] 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
[ 56%] 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
[ 56%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/nxsdistancesblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 57%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 58%] 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
[ 58%] 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
[ 59%] 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
[ 60%] 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/nxssetreader.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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'
[ 60%] Built target yaml-cpp
make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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'
[ 60%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pda/gurobiwrapper.cpp:24:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 60%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/phylo-yaml/statespace.cpp:12:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
[ 62%] 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/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
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
[ 62%] 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
[ 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/ncl/nxstreesblock.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 64%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
[ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.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
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
[ 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/pda/pdnetwork.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 66%] 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/pda/pdtree.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 66%] 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'
[ 66%] 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'
[ 66%] 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
[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
[ 67%] 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
[ 67%] 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/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
[ 68%] 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/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
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
[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.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
[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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%] 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/alignment/alignment.cpp:12:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 69%] 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'
[ 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.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'
[ 69%] 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
[ 70%] 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 model/CMakeFiles/model.dir/modeldna.cpp.o
[ 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/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
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
[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.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/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
[ 73%] 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'
[ 73%] Built target phyloYAML
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modeldna.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/modelmarkov.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 74%] 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
/usr/bin/ranlib libpda.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 74%] 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'
/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 -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build
make[4]: Entering directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 75%] 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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);
| ^~~~~
/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__;
| ^~~~~~~~
/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*);
| ^~~~~
/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) {
| ^~~~~
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/rategammainvar.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/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
[ 76%] 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
/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/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/main.cpp:37:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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
[ 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
[ 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
[ 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
[ 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/ratemeyerdiscrete.cpp:21:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/ratemeyerhaeseler.cpp:20:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*) {
| ^~~~~
[ 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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
/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.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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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) {
| ^~~~~
[ 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 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
[ 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
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/phylotesting.cpp:15:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
/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/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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
[ 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.mpi'
[ 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.mpi'
[ 85%] Built target kernelavx
[ 86%] Linking CXX static library libmain.a
cd /build/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
cd /build/iqtree-2.0.7+dfsg/build.mpi/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
[ 86%] Linking CXX static library libalignment.a
cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
cd /build/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
/usr/bin/ranlib libmain.a
/usr/bin/ranlib libalignment.a
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
make[4]: Leaving directory '/build/iqtree-2.0.7+dfsg/build.mpi'
[ 86%] Built target main
[ 86%] Built target alignment
[ 87%] Linking CXX static library libmodel.a
cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
cd /build/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1
/usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o
/usr/bin/ranlib libmodel.a
make[4]: Leaving directory '/build/iqtree-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
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
[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.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
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.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/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
[ 89%] 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/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/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
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.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
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.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/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
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
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
[ 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/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
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
[ 92%] 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/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/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/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.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
[ 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/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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/phylotree.cpp:22:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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
| ^~~~~~~~~~~~~~~
[ 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
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*);
| ^~~~~
[ 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*);
| ^~~~~
[ 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
[ 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
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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/phylotreepars.cpp:10:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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 | }
| ^
[ 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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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.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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/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/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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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*);
| ^~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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/discordance.cpp:8:
/build/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
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 ...
+ time /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: ionos15-amd64 (AVX, 47 GB RAM)
Command: /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy
Seed: 540558 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sun May 26 20:48:54 2024
Kernel: AVX - 1 threads (16 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 16 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)... 0.013 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: -11278.874
Optimal log-likelihood: -11278.756
Rate parameters: A-C: 1.52235 A-G: 2.37813 A-T: 1.75542 C-G: 1.90960 C-T: 2.99649 G-T: 1.00000
Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239
Proportion of invariable sites: 0.084
Gamma shape alpha: 1.409
Parameters optimization took 1 rounds (0.194 sec)
Time for fast ML tree search: 2.472 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 11872.018 93 23930.037 23990.326 24297.446
2 GTR+F+I 11620.575 94 23429.149 23490.949 23800.510
3 GTR+F+G4 11292.573 94 22773.146 22834.945 23144.506
4 GTR+F+I+G4 11278.761 95 22747.521 22810.855 23122.832
5 GTR+F+R2 11401.184 95 22992.368 23055.701 23367.679
6 GTR+F+R3 11281.109 97 22756.217 22822.693 23139.430
7 GTR+F+R4 11272.436 99 22742.872 22812.590 23133.986
8 GTR+F+R5 11272.103 101 22746.206 22819.270 23145.221
17 SYM+I+G4 11284.886 92 22753.772 22812.577 23117.232
30 TVM+F+I+G4 11282.889 94 22753.778 22815.577 23125.138
43 TVMe+I+G4 11288.282 91 22758.564 22815.907 23118.073
56 TIM3+F+I+G4 11291.857 93 22769.714 22830.004 23137.124
69 TIM3e+I+G4 11298.317 90 22776.635 22832.539 23132.193
82 TIM2+F+I+G4 11295.475 93 22776.950 22837.240 23144.360
95 TIM2e+I+G4 11306.047 90 22792.094 22847.999 23147.652
108 TIM+F+I+G4 11285.258 93 22756.516 22816.806 23123.926
121 TIMe+I+G4 11295.055 90 22770.110 22826.015 23125.668
134 TPM3u+F+I+G4 11296.211 92 22776.422 22835.226 23139.881
147 TPM3+F+I+G4 11296.211 92 22776.422 22835.226 23139.881
160 TPM2u+F+I+G4 11299.660 92 22783.320 22842.124 23146.779
173 TPM2+F+I+G4 11299.660 92 22783.320 22842.124 23146.779
186 K3Pu+F+I+G4 11289.410 92 22762.821 22821.625 23126.280
199 K3P+I+G4 11298.327 89 22774.654 22829.144 23126.261
212 TN+F+I+G4 11296.048 92 22776.096 22834.900 23139.555
225 TNe+I+G4 11306.431 89 22790.861 22845.351 23142.468
238 HKY+F+I+G4 11300.314 91 22782.628 22839.971 23142.137
251 K2P+I+G4 11309.812 88 22795.624 22848.722 23143.281
264 F81+F+I+G4 11353.444 90 22886.889 22942.793 23242.447
277 JC+I+G4 11360.402 87 22894.804 22946.534 23238.510
Akaike Information Criterion: GTR+F+R4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: SYM+I+G4
Best-fit model: SYM+I+G4 chosen according to BIC
All model information printed to example.phy.model.gz
CPU time for ModelFinder: 9.092 seconds (0h:0m:9s)
Wall-clock time for ModelFinder: 30.177 seconds (0h:0m:30s)
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, 1.445 / Estimate: 0.000, 0.890 / LogL: -11298.276
Init pinv, alpha: 0.012, 1.445 / Estimate: 0.083, 1.432 / LogL: -11284.881
Init pinv, alpha: 0.023, 1.445 / Estimate: 0.083, 1.430 / LogL: -11284.879
Init pinv, alpha: 0.035, 1.445 / Estimate: 0.083, 1.431 / LogL: -11284.885
Init pinv, alpha: 0.046, 1.445 / Estimate: 0.083, 1.435 / LogL: -11284.879
Init pinv, alpha: 0.058, 1.445 / Estimate: 0.083, 1.432 / LogL: -11284.877
Init pinv, alpha: 0.069, 1.445 / Estimate: 0.083, 1.429 / LogL: -11284.887
Init pinv, alpha: 0.081, 1.445 / Estimate: 0.083, 1.435 / LogL: -11284.873
Init pinv, alpha: 0.093, 1.445 / Estimate: 0.085, 1.449 / LogL: -11284.882
Init pinv, alpha: 0.104, 1.445 / Estimate: 0.085, 1.455 / LogL: -11284.890
Optimal pinv,alpha: 0.083, 1.435 / LogL: -11284.873
Parameters optimization took 9.160 sec
Computing ML distances based on estimated model parameters... 0.059 sec
Computing BIONJ tree...
0.002 seconds
Log-likelihood of BIONJ tree: -11269.983
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 1.982 second
Computing log-likelihood of 98 initial trees ... 5.810 seconds
Current best score: -11253.469
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -11222.937
Iteration 10 / LogL: -11229.927 / Time: 0h:0m:29s
Iteration 20 / LogL: -11230.124 / Time: 0h:0m:42s
Finish initializing candidate tree set (13)
Current best tree score: -11222.937 / CPU time: 33.336
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 24: -11222.757
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 30: -11222.594
Iteration 30 / LogL: -11222.594 / Time: 0h:1m:3s (0h:3m:37s left)
Iteration 40 / LogL: -11222.761 / Time: 0h:1m:21s (0h:3m:7s left)
Iteration 50 / LogL: -11224.270 / Time: 0h:1m:38s (0h:2m:40s left)
Iteration 60 / LogL: -11235.178 / Time: 0h:1m:55s (0h:2m:16s left)
Iteration 70 / LogL: -11222.629 / Time: 0h:2m:8s (0h:1m:51s left)
Iteration 80 / LogL: -11224.197 / Time: 0h:2m:18s (0h:1m:27s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 89: -11222.113
Iteration 90 / LogL: -11224.793 / Time: 0h:2m:37s (0h:2m:55s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 96: -11221.031
Iteration 100 / LogL: -11222.270 / Time: 0h:2m:54s (0h:2m:49s left)
Iteration 110 / LogL: -11222.150 / Time: 0h:3m:11s (0h:2m:31s left)
Iteration 120 / LogL: -11228.334 / Time: 0h:3m:24s (0h:2m:10s left)
Estimate model parameters (epsilon = 0.100)
UPDATE BEST LOG-LIKELIHOOD: -11220.898
Iteration 130 / LogL: -11220.904 / Time: 0h:3m:33s (0h:1m:49s left)
Iteration 140 / LogL: -11222.276 / Time: 0h:3m:40s (0h:1m:28s left)
Iteration 150 / LogL: -11235.135 / Time: 0h:3m:46s (0h:1m:9s left)
Iteration 160 / LogL: -11220.937 / Time: 0h:3m:52s (0h:0m:52s left)
Iteration 170 / LogL: -11233.341 / Time: 0h:3m:57s (0h:0m:36s left)
Iteration 180 / LogL: -11221.695 / Time: 0h:4m:2s (0h:0m:21s left)
Iteration 190 / LogL: -11221.276 / Time: 0h:4m:9s (0h:0m:7s left)
TREE SEARCH COMPLETED AFTER 197 ITERATIONS / Time: 0h:4m:14s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -11220.898
Optimal log-likelihood: -11220.892
Rate parameters: A-C: 1.52930 A-G: 2.42612 A-T: 1.66909 C-G: 2.00225 C-T: 2.84350 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Proportion of invariable sites: 0.084
Gamma shape alpha: 1.533
Parameters optimization took 1 rounds (0.109 sec)
BEST SCORE FOUND : -11220.892
Total tree length: 12.595
Total number of iterations: 197
CPU time used for tree search: 102.676 sec (0h:1m:42s)
Wall-clock time used for tree search: 245.151 sec (0h:4m:5s)
Total CPU time used: 106.408 sec (0h:1m:46s)
Total wall-clock time used: 254.800 sec (0h:4m:14s)
Analysis results written to:
IQ-TREE report: example.phy.iqtree
Maximum-likelihood tree: example.phy.treefile
Likelihood distances: example.phy.mldist
Screen log file: example.phy.log
Date and Time: Sun May 26 20:53:39 2024
115.51user 1.52system 4:45.05elapsed 41%CPU (0avgtext+0avgdata 14216maxresident)k
64inputs+0outputs (4major+2016minor)pagefaults 0swaps
+ time /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: ionos15-amd64 (AVX, 47 GB RAM)
Command: /build/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo
Seed: 584878 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Sun May 26 20:53:39 2024
Kernel: AVX - 1 threads (16 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 16 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)... 0.008 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: -11222.583
Optimal log-likelihood: -11222.469
Rate parameters: A-C: 1.46888 A-G: 2.34107 A-T: 1.77635 C-G: 1.90931 C-T: 2.84690 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: 1.531
Parameters optimization took 1 rounds (0.087 sec)
Time for fast ML tree search: 1.028 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 11784.865 93 23755.731 23816.021 24123.141
2 GTR+F+I 11542.762 94 23273.525 23335.324 23644.885
3 GTR+F+G4 11238.124 94 22664.249 22726.048 23035.609
4 GTR+F+I+G4 11222.470 95 22634.941 22698.274 23010.252
5 GTR+F+R2 11332.079 95 22854.159 22917.492 23229.470
6 GTR+F+R3 11222.904 97 22639.808 22706.283 23023.020
7 GTR+F+R4 11216.558 99 22631.117 22700.835 23022.231
8 GTR+F+R5 11216.196 101 22634.392 22707.456 23033.407
17 SYM+I+G4 11225.577 92 22635.154 22693.958 22998.613
30 TVM+F+I+G4 11225.427 94 22638.855 22700.654 23010.215
43 TVMe+I+G4 11227.870 91 22637.741 22695.083 22997.249
56 TIM3+F+I+G4 11237.296 93 22660.592 22720.881 23028.001
69 TIM3e+I+G4 11240.994 90 22661.988 22717.892 23017.545
82 TIM2+F+I+G4 11240.874 93 22667.748 22728.038 23035.158
95 TIM2e+I+G4 11248.653 90 22677.305 22733.210 23032.863
108 TIM+F+I+G4 11228.664 93 22643.327 22703.617 23010.737
121 TIMe+I+G4 11235.522 90 22651.043 22706.948 23006.601
134 TPM3u+F+I+G4 11240.439 92 22664.878 22723.682 23028.337
147 TPM3+F+I+G4 11240.439 92 22664.878 22723.682 23028.337
160 TPM2u+F+I+G4 11243.911 92 22671.821 22730.625 23035.280
173 TPM2+F+I+G4 11243.911 92 22671.821 22730.625 23035.280
186 K3Pu+F+I+G4 11231.608 92 22647.215 22706.019 23010.674
199 K3P+I+G4 11237.658 89 22653.317 22707.806 23004.924
212 TN+F+I+G4 11241.228 92 22666.457 22725.261 23029.916
225 TNe+I+G4 11248.858 89 22675.716 22730.205 23027.323
238 HKY+F+I+G4 11244.294 91 22670.587 22727.930 23030.096
251 K2P+I+G4 11251.083 88 22678.166 22731.264 23025.823
264 F81+F+I+G4 11294.363 90 22768.726 22824.630 23124.283
277 JC+I+G4 11298.377 87 22770.754 22822.484 23114.460
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: 7.627 seconds (0h:0m:7s)
Wall-clock time for ModelFinder: 8.468 seconds (0h:0m:8s)
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, 1.576 / Estimate: 0.000, 0.961 / LogL: -11242.445
Init pinv, alpha: 0.012, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.870
Init pinv, alpha: 0.023, 1.576 / Estimate: 0.084, 1.565 / LogL: -11227.872
Init pinv, alpha: 0.035, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.874
Init pinv, alpha: 0.046, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.872
Init pinv, alpha: 0.058, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.875
Init pinv, alpha: 0.069, 1.576 / Estimate: 0.083, 1.562 / LogL: -11227.877
Init pinv, alpha: 0.081, 1.576 / Estimate: 0.084, 1.566 / LogL: -11227.871
Init pinv, alpha: 0.093, 1.576 / Estimate: 0.085, 1.579 / LogL: -11227.871
Init pinv, alpha: 0.104, 1.576 / Estimate: 0.085, 1.585 / LogL: -11227.877
Optimal pinv,alpha: 0.084, 1.568 / LogL: -11227.870
Parameters optimization took 3.642 sec
Computing ML distances based on estimated model parameters... 0.058 sec
Computing BIONJ tree...
0.006 seconds
Log-likelihood of BIONJ tree: -11270.856
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.944 second
Computing log-likelihood of 98 initial trees ... 3.010 seconds
Current best score: -11227.870
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -11226.734
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 2: -11225.137
Iteration 10 / LogL: -11226.927 / Time: 0h:0m:12s
Iteration 20 / LogL: -11226.926 / Time: 0h:0m:18s
Finish initializing candidate tree set (13)
Current best tree score: -11225.137 / CPU time: 14.283
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Iteration 30 / LogL: -11235.709 / Time: 0h:0m:27s (0h:1m:7s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 33: -11222.904
Iteration 40 / LogL: -11225.506 / Time: 0h:0m:41s (0h:1m:39s left)
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 44: -11222.785
Iteration 50 / LogL: -11223.077 / Time: 0h:0m:58s (0h:1m:53s left)
Iteration 60 / LogL: -11223.003 / Time: 0h:1m:13s (0h:1m:44s left)
Iteration 70 / LogL: -11222.870 / Time: 0h:1m:23s (0h:1m:29s left)
Iteration 80 / LogL: -11222.829 / Time: 0h:1m:35s (0h:1m:17s left)
Iteration 90 / LogL: -11228.753 / Time: 0h:1m:49s (0h:1m:6s left)
Iteration 100 / LogL: -11222.943 / Time: 0h:2m:3s (0h:0m:54s left)
Iteration 110 / LogL: -11226.133 / Time: 0h:2m:13s (0h:0m:41s left)
Iteration 120 / LogL: -11222.800 / Time: 0h:2m:34s (0h:0m:31s left)
Iteration 130 / LogL: -11223.251 / Time: 0h:2m:48s (0h:0m:18s left)
Iteration 140 / LogL: -11223.621 / Time: 0h:3m:3s (0h:0m:5s left)
TREE SEARCH COMPLETED AFTER 145 ITERATIONS / Time: 0h:3m:9s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -11222.785
Optimal log-likelihood: -11222.781
Rate parameters: A-C: 1.54136 A-G: 2.64404 A-T: 1.70145 C-G: 2.01309 C-T: 2.64404 G-T: 1.00000
Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250
Proportion of invariable sites: 0.083
Gamma shape alpha: 1.529
Parameters optimization took 1 rounds (0.126 sec)
BEST SCORE FOUND : -11222.781
Total tree length: 12.598
Total number of iterations: 145
CPU time used for tree search: 78.514 sec (0h:1m:18s)
Wall-clock time used for tree search: 185.395 sec (0h:3m:5s)
Total CPU time used: 81.814 sec (0h:1m:21s)
Total wall-clock time used: 189.394 sec (0h:3m:9s)
Analysis results written to:
IQ-TREE report: example.phy.iqtree
Maximum-likelihood tree: example.phy.treefile
Likelihood distances: example.phy.mldist
Screen log file: example.phy.log
Date and Time: Sun May 26 20:56:57 2024
89.44user 0.95system 3:17.88elapsed 45%CPU (0avgtext+0avgdata 14676maxresident)k
0inputs+0outputs (0major+3579minor)pagefaults 0swaps
+ rm -rf /tmp/iqtree-test.oKRBCq
204.98user 2.54system 8:03.91elapsed 42%CPU (0avgtext+0avgdata 14676maxresident)k
1152inputs+0outputs (54major+7075minor)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 -j16 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 -j16 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-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'.
dpkg-deb: building package 'iqtree' in '../iqtree_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: 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/2789017 and its subdirectories
I: Current time: Sun May 26 21:05:53 -12 2024
I: pbuilder-time-stamp: 1716800753
Tue Apr 25 02:42:55 UTC 2023 I: 1st build successful. Starting 2nd build on remote node ionos1-amd64.debian.net.
Tue Apr 25 02:42:55 UTC 2023 I: Preparing to do remote build '2' on ionos1-amd64.debian.net.
Tue Apr 25 03:05:00 UTC 2023 I: Deleting $TMPDIR on ionos1-amd64.debian.net.
Tue Apr 25 03:05:01 UTC 2023 I: iqtree_2.0.7+dfsg-1_amd64.changes:
Format: 1.8
Date: Fri, 21 Jan 2022 12:05:21 +0100
Source: iqtree
Binary: iqtree iqtree-dbgsym
Architecture: amd64
Version: 2.0.7+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
iqtree - efficient phylogenetic software by maximum likelihood
Changes:
iqtree (2.0.7+dfsg-1) unstable; urgency=medium
.
[ Andreas Tille ]
* New upstream version
* debhelper-compat 13 (routine-update)
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Build-Depends: libboost-dev
* Executables are now named iqtree2
* Drop invalid option `-omp` from build time test
.
[ Steffen Moeller ]
* Fix watchfile to detect new versions on github (routine-update)
* Standards-Version: 4.6.0
Checksums-Sha1:
d23d4e1efce7e2976f9c694aff4a5e74a178d928 87290256 iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb
af69a1f7a1795e7d53a9810cdea3ef7d234c8208 8019 iqtree_2.0.7+dfsg-1_amd64.buildinfo
c2969ee631668699c0e78e9cc521fdbd8862e61e 3533488 iqtree_2.0.7+dfsg-1_amd64.deb
Checksums-Sha256:
71fe84f541f2a1d33cb1a5303221ede0a18dac5f55f90cd57f1ce173745f48af 87290256 iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb
b218ec67320ef3e19645bf49afe651180b113f0841863c2cf98f7cce3c15561b 8019 iqtree_2.0.7+dfsg-1_amd64.buildinfo
abce2956711be1afb34e226158ef997c2fa63e239005240aea0838e2c90ac8a4 3533488 iqtree_2.0.7+dfsg-1_amd64.deb
Files:
c5aec400218b90dc1c667da5ac0412da 87290256 debug optional iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb
4cbc0849bb56294f2a5749204f6bee32 8019 science optional iqtree_2.0.7+dfsg-1_amd64.buildinfo
0f4b3070885e6a6fa91a11308b34c55f 3533488 science optional iqtree_2.0.7+dfsg-1_amd64.deb
Tue Apr 25 03:05:03 UTC 2023 I: diffoscope 241 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/iqtree_2.0.7+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/iqtree_2.0.7+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/iqtree_2.0.7+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b1/iqtree_2.0.7+dfsg-1_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.aPoyGWrE/b2/iqtree_2.0.7+dfsg-1_amd64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 3.712s)
3.712s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 3.343s)
3.343s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Tue Apr 25 03:05:10 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists.
Tue Apr 25 03:05:10 UTC 2023 I: iqtree from bookworm built successfully and reproducibly on amd64.
Tue Apr 25 03:05:14 UTC 2023 I: Submitting .buildinfo files to external archives:
Tue Apr 25 03:05:14 UTC 2023 I: Submitting 12K b1/iqtree_2.0.7+dfsg-1_amd64.buildinfo.asc
Tue Apr 25 03:05:15 UTC 2023 I: Submitting 12K b2/iqtree_2.0.7+dfsg-1_amd64.buildinfo.asc
Tue Apr 25 03:05:17 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Tue Apr 25 03:05:17 UTC 2023 I: Done submitting .buildinfo files.
Tue Apr 25 03:05:17 UTC 2023 I: Removing signed iqtree_2.0.7+dfsg-1_amd64.buildinfo.asc files:
removed './b1/iqtree_2.0.7+dfsg-1_amd64.buildinfo.asc'
removed './b2/iqtree_2.0.7+dfsg-1_amd64.buildinfo.asc'