I: pbuilder: network access will be disabled during build
I: Current time: Thu Feb 27 11:11:12 -12 2025
I: pbuilder-time-stamp: 1740697872
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job
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
dpkg-source: warning: cannot verify inline signature for ./iqtree_2.0.7+dfsg-1.dsc: unsupported subcommand
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/30737/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='i386'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 '
DISTRIBUTION='trixie'
HOME='/root'
HOST_ARCH='i386'
IFS='
'
INVOCATION_ID='2a034d560a294c9d8e043c09bfe924db'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
LD_LIBRARY_PATH='/usr/lib/libeatmydata'
LD_PRELOAD='libeatmydata.so'
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='30737'
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.I8nAc8Lk/pbuilderrc_YZRW --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.I8nAc8Lk/b1 --logfile b1/build.log iqtree_2.0.7+dfsg-1.dsc'
SUDO_GID='112'
SUDO_UID='107'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://46.16.76.132:3128'
I: uname -a
Linux ionos2-i386 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) x86_64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/30737/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: i386
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 ... 19789 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-14{a} gfortran-14-i686-linux-gnu{a} groff-base{a} help2man{a} hwloc-nox{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libeigen3-dev{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran-14-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhwloc-dev{a} libhwloc15{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmpich-dev{a} libmpich12{a} libnghttp2-14{a} libnghttp3-9{a} libnuma-dev{a} libnuma1{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libslurm42t64{a} libsprng2{a} libsprng2-dev{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} mpi-default-dev{a} mpich{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 krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 92 newly installed, 0 to remove and 0 not upgraded.
Need to get 76.8 MB of archives. After unpacking 404 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian trixie/main i386 liblocale-gettext-perl i386 1.07-7+b1 [15.4 kB]
Get: 2 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-7 [66.0 kB]
Get: 3 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-7 [876 kB]
Get: 4 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 6 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 7 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 8 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.23.1-1 [245 kB]
Get: 9 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 10 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB]
Get: 11 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.4-4 [96.4 kB]
Get: 12 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 13 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 14 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-5 [301 kB]
Get: 15 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB]
Get: 16 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 17 http://deb.debian.org/debian trixie/main i386 automake all 1:1.17-3 [862 kB]
Get: 18 http://deb.debian.org/debian trixie/main i386 autopoint all 0.23.1-1 [770 kB]
Get: 19 http://deb.debian.org/debian trixie/main i386 chrpath i386 0.18-1 [14.0 kB]
Get: 20 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.31.5-2 [2267 kB]
Get: 21 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-6 [9582 kB]
Get: 22 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b2 [734 kB]
Get: 23 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB]
Get: 24 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB]
Get: 25 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-4 [35.0 kB]
Get: 26 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2-1 [24.3 kB]
Get: 27 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-4 [83.7 kB]
Get: 28 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 29 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-4 [354 kB]
Get: 30 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-4 [149 kB]
Get: 31 http://deb.debian.org/debian trixie/main i386 libunistring5 i386 1.3-1 [458 kB]
Get: 32 http://deb.debian.org/debian trixie/main i386 libidn2-0 i386 2.3.7-2+b1 [130 kB]
Get: 33 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8+b1 [20.9 kB]
Get: 34 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8+b1 [61.3 kB]
Get: 35 http://deb.debian.org/debian trixie/main i386 libldap2 i386 2.6.9+dfsg-1 [205 kB]
Get: 36 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 37 http://deb.debian.org/debian trixie/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 38 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 39 http://deb.debian.org/debian trixie/main i386 libffi8 i386 3.4.7-1 [21.4 kB]
Get: 40 http://deb.debian.org/debian trixie/main i386 libp11-kit0 i386 0.25.5-3 [423 kB]
Get: 41 http://deb.debian.org/debian trixie/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get: 42 http://deb.debian.org/debian trixie/main i386 libgnutls30t64 i386 3.8.9-2 [1462 kB]
Get: 43 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 44 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 45 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.12.1-2 [415 kB]
Get: 46 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 47 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB]
Get: 48 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB]
Get: 49 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.50.0-2 [163 kB]
Get: 50 http://deb.debian.org/debian trixie/main i386 cmake i386 3.31.5-2 [13.1 MB]
Get: 51 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 52 http://deb.debian.org/debian trixie/main i386 libtool all 2.5.4-3 [539 kB]
Get: 53 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 54 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 55 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 56 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 57 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 58 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 59 http://deb.debian.org/debian trixie/main i386 gettext i386 0.23.1-1 [1714 kB]
Get: 60 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 61 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 62 http://deb.debian.org/debian trixie/main i386 debhelper all 13.24.1 [920 kB]
Get: 63 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-16 [735 kB]
Get: 64 http://deb.debian.org/debian trixie/main i386 libgfortran-14-dev i386 14.2.0-16 [800 kB]
Get: 65 http://deb.debian.org/debian trixie/main i386 gfortran-14-i686-linux-gnu i386 14.2.0-16 [12.5 MB]
Get: 66 http://deb.debian.org/debian trixie/main i386 gfortran-14 i386 14.2.0-16 [13.6 kB]
Get: 67 http://deb.debian.org/debian trixie/main i386 help2man i386 1.49.3 [198 kB]
Get: 68 http://deb.debian.org/debian trixie/main i386 libhwloc15 i386 2.12.0-1 [177 kB]
Get: 69 http://deb.debian.org/debian trixie/main i386 hwloc-nox i386 2.12.0-1 [232 kB]
Get: 70 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-4.1+b1 [10.6 MB]
Get: 71 http://deb.debian.org/debian trixie/main i386 libboost-dev i386 1.83.0.2+b2 [3840 B]
Get: 72 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 73 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 74 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 75 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-4 [14.0 kB]
Get: 76 http://deb.debian.org/debian trixie/main i386 libeigen3-dev all 3.4.0-4 [1041 kB]
Get: 77 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-3 [329 kB]
Get: 78 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-3 [661 kB]
Get: 79 http://deb.debian.org/debian trixie/main i386 libnuma1 i386 2.0.18-1+b1 [23.9 kB]
Get: 80 http://deb.debian.org/debian trixie/main i386 libnuma-dev i386 2.0.18-1+b1 [38.8 kB]
Get: 81 http://deb.debian.org/debian trixie/main i386 libltdl7 i386 2.5.4-3 [417 kB]
Get: 82 http://deb.debian.org/debian trixie/main i386 libltdl-dev i386 2.5.4-3 [169 kB]
Get: 83 http://deb.debian.org/debian trixie/main i386 libhwloc-dev i386 2.12.0-1 [273 kB]
Get: 84 http://deb.debian.org/debian trixie/main i386 libmpich12 i386 4.2.1-5 [1519 kB]
Get: 85 http://deb.debian.org/debian trixie/main i386 libslurm42t64 i386 24.11.0-2 [754 kB]
Get: 86 http://deb.debian.org/debian trixie/main i386 mpich i386 4.2.1-5 [236 kB]
Get: 87 http://deb.debian.org/debian trixie/main i386 libmpich-dev i386 4.2.1-5 [2503 kB]
Get: 88 http://deb.debian.org/debian trixie/main i386 libsprng2 i386 2.0a-16 [79.6 kB]
Get: 89 http://deb.debian.org/debian trixie/main i386 libsprng2-dev i386 2.0a-16 [82.9 kB]
Get: 90 http://deb.debian.org/debian trixie/main i386 mpi-default-dev i386 1.18 [3372 B]
Get: 91 http://deb.debian.org/debian trixie/main i386 time i386 1.9-0.2 [50.9 kB]
Get: 92 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Fetched 76.8 MB in 1s (70.5 MB/s)
Preconfiguring packages ...
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(Reading database ... 19789 files and directories currently installed.)
Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b1_i386.deb ...
Unpacking liblocale-gettext-perl (1.07-7+b1) ...
Selecting previously unselected package libproc2-0:i386.
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Unpacking libproc2-0:i386 (2:4.0.4-7) ...
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Preparing to unpack .../02-procps_2%3a4.0.4-7_i386.deb ...
Unpacking procps (2:4.0.4-7) ...
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Unpacking sensible-utils (0.0.24) ...
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Unpacking libmagic-mgc (1:5.45-3+b1) ...
Selecting previously unselected package libmagic1t64:i386.
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Unpacking libmagic1t64:i386 (1:5.45-3+b1) ...
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Unpacking file (1:5.45-3+b1) ...
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Unpacking gettext-base (0.23.1-1) ...
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Unpacking libuchardet0:i386 (0.0.8-1+b2) ...
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Unpacking groff-base (1.23.0-7) ...
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Unpacking bsdextrautils (2.40.4-4) ...
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Unpacking libpipeline1:i386 (1.5.8-1) ...
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update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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update-alternatives: using /usr/include/i386-linux-gnu/mpich to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode
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Reading package lists...
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/reproducible-path/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 i386
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg'
dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp"
cd build.omp && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu -DIQTREE_FLAGS=omp ..
CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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
CMake Warning (dev) at CMakeLists.txt:74 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/i386-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0")
IQ-TREE flags : omp
Target OS : Unix
Compiler : GNU Compiler (gcc)
Target binary : 32-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/i386-linux-gnu/libz.so (found version "1.3.1")
Using system zlib
CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- clang-tidy not found.
-- Configuring done (2.5s)
-- Generating done (0.2s)
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/reproducible-path/iqtree-2.0.7+dfsg/build.omp
dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS=""
cd build.serial && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu -DIQTREE_FLAGS= ..
CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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
CMake Warning (dev) at CMakeLists.txt:74 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/i386-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0")
IQ-TREE flags :
Target OS : Unix
Compiler : GNU Compiler (gcc)
Target binary : 32-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/i386-linux-gnu/libz.so (found version "1.3.1")
Using system zlib
CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- clang-tidy not found.
-- Configuring done (3.0s)
-- Generating done (0.2s)
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/reproducible-path/iqtree-2.0.7+dfsg/build.serial
dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi"
cd build.mpi && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu -DIQTREE_FLAGS=mpi ..
CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- 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
CMake Warning (dev) at CMakeLists.txt:74 (find_package):
Policy CMP0167 is not set: The FindBoost module is removed. Run "cmake
--help-policy CMP0167" for policy details. Use the cmake_policy command to
set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found Boost: /usr/lib/i386-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0")
IQ-TREE flags : mpi
Target OS : Unix
Compiler : GNU Compiler (gcc)
-- Found MPI_C: /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so (found version "4.1")
-- Found MPI_CXX: /usr/lib/i386-linux-gnu/mpich/lib/libmpichcxx.so (found version "4.1")
-- Found MPI: TRUE (found version "4.1")
Target binary : 32-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/i386-linux-gnu/libz.so (found version "1.3.1")
Using system zlib
CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- Performing Test FLAG_WEXTRA
-- Performing Test FLAG_WEXTRA - Success
CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required):
Compatibility with CMake < 3.10 will be removed from a future version of
CMake.
Update the VERSION argument <min> value. Or, use the <min>...<max> syntax
to tell CMake that the project requires at least <min> but has been updated
to work with policies introduced by <max> or earlier.
-- clang-tidy not found.
-- Configuring done (4.4s)
-- Generating done (0.2s)
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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi
dh override_dh_auto_configure
make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
dh_auto_build -Bbuild.omp
cd build.omp && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
/usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend
make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color="
make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color="
make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/reproducible-path/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
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color="
make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color="
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make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
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make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color="
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[ 0%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
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make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
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make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 2%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
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make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
[ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
[ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp
[ 4%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c
[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
[ 4%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp
[ 4%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40:
/build/reproducible-path/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 sprng/CMakeFiles/sprng.dir/makeseed.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c
[ 5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c
[ 6%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c
[ 7%] Linking CXX static library libvectorclass.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1
[ 7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c
/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
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[ 7%] Built target vectorclass
make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend
[ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color="
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c
[ 8%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp
[ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp
[ 10%] Building C object booster/CMakeFiles/booster.dir/io.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF':
/build/reproducible-path/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/reproducible-path/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));
| ^~~~~~~~~~~~~~~~~~
[ 11%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c
[ 11%] Building C object booster/CMakeFiles/booster.dir/sort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c
[ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp
[ 11%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c
[ 11%] Linking C static library libsprng.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
/usr/bin/ranlib libsprng.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 12%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c
[ 12%] Built target sprng
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 12%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c
[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 12%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT':
/build/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp
[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp
[ 14%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c
[ 15%] Linking CXX static library libgsl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 15%] Built target gsl
[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp
[ 16%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c
[ 17%] Building C object booster/CMakeFiles/booster.dir/booster.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c
[ 18%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c
/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu':
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 18%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c
[ 18%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp
[ 18%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c
[ 19%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp
[ 20%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c
[ 20%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c
[ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c
[ 20%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c
[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT':
/build/reproducible-path/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/reproducible-path/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));
| ^~~~~~~~~~~~~~~~~~
[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c
[ 23%] Building C object pll/CMakeFiles/pll.dir/models.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c
[ 23%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp
[ 23%] Building C object booster/CMakeFiles/booster.dir/stats.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c
[ 23%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp
[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp
[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp
[ 25%] Linking CXX static library liblbfgsb.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1
[ 26%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c
/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
/usr/bin/ranlib liblbfgsb.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 26%] Built target lbfgsb
make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color="
/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData':
/build/reproducible-path/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/reproducible-path/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 );
| ^~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 27%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp
[ 27%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c
[ 28%] Linking C static library libbooster.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 28%] Built target booster
[ 28%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp
[ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c
[ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 29%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c
[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp
[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
/build/reproducible-path/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++/14/bits/stl_function.h:1435:
/usr/include/c++/14/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp
[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp
[ 31%] Linking CXX static library libwhtest.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake
[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1
/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
/usr/bin/ranlib libwhtest.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 31%] Built target whtest
[ 31%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
[ 32%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c
[ 32%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c
[ 32%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp
[ 33%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp
[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp
[ 34%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c
[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42:
/build/reproducible-path/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/queue.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 34%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
/build/reproducible-path/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/recom.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43:
/build/reproducible-path/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/clamped_uint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp
[ 36%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c
[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp
[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47:
/build/reproducible-path/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/searchAlgo.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp
[ 40%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp
[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp
[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp
[ 41%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c
[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp
[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp
[ 41%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp
[ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp
[ 43%] Building C object pll/CMakeFiles/pll.dir/stack.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c
[ 43%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c
[ 43%] Building C object pll/CMakeFiles/pll.dir/trash.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 44%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49:
/build/reproducible-path/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 terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp
[ 45%] Building C object pll/CMakeFiles/pll.dir/utils.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c
[ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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) *
| ^~~~~~~~~~~~~~~~~~
[ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp
[ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp
[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp
[ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp
[ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp
[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp
[ 48%] Linking CXX static library libnclextra.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 48%] Built target nclextra
make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 48%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp
[ 49%] Linking C static library libpll.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1
[ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 49%] Built target pll
[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp
[ 49%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp
[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp
[ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp
[ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp
[ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp
[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp
[ 55%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp
[ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp
[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp
[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp
[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp
[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp
[ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 58%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp
[ 58%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp
[ 58%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 59%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 60%] Linking CXX static library libyaml-cpp.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1
[ 60%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 60%] Built target yaml-cpp
make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 60%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp
[ 61%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp
[ 62%] Linking CXX static library libterraphast.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1
[ 63%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 63%] Built target terraphast
[ 64%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp
[ 64%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp
[ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp
[ 65%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/map:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c
[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp
[ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp
[ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp
[ 67%] Linking CXX static library libncl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
/usr/bin/ranlib libncl.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 67%] Built target ncl
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /usr/include/boost/math/distributions/binomial.hpp:83,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
[ 68%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp
[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp
[ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp
[ 71%] Linking CXX static library libutils.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 71%] Built target utils
make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color="
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 71%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp
[ 72%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp
[ 73%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 73%] Linking CXX static library libphyloYAML.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1
[ 73%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp
/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o
/usr/bin/ranlib libphyloYAML.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 73%] Built target phyloYAML
[ 74%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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) {
| ^~~~~
[ 74%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/modelsubst.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 76%] Linking CXX static library libpda.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
[ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26:
/build/reproducible-path/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*);
| ^~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 76%] Built target pda
make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 77%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 78%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp
[ 78%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp
[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/rateinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp
[ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp
[ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp
[ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp
[ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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) {
| ^~~~~
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 85%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 85%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp
[ 85%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /usr/include/c++/14/complex:45,
from /usr/include/eigen3/Eigen/Core:50,
from /usr/include/eigen3/Eigen/Dense:1,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 85%] 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
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
/usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
/usr/bin/ranlib libkernelsse.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 85%] Built target kernelsse
[ 86%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp
[ 86%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type]
180 | }
| ^
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type]
257 | }
| ^
[ 87%] Linking CXX static library libmain.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 87%] Built target main
[ 87%] Linking CXX static library libalignment.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 87%] Built target alignment
[ 88%] Linking CXX static library libmodel.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 88%] Built target model
make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp
[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type]
653 | }
| ^
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)':
/build/reproducible-path/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/quartet.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp
[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 97%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp
[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp
[ 98%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 98%] Linking CXX static library libtree.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[100%] Linking CXX static library libterrace.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[100%] Built target terrace
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib32 -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib32: 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 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/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
[100%] Built target iqtree2
make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles 0
make[2]: Leaving directory '/build/reproducible-path/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
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make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
/usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks
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make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend
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make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color="
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make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color="
make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend
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make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color="
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make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
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make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color="
make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend
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[ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
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make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color="
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build
[ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
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[ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp
make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
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make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
[ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c
[ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
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make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp
[ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c
[ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp
[ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp
[ 4%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o
[ 4%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp
[ 4%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF':
/build/reproducible-path/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/reproducible-path/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));
| ^~~~~~~~~~~~~~~~~~
[ 5%] Linking CXX static library libvectorclass.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1
[ 5%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c
/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
/usr/bin/ranlib libvectorclass.a
[ 6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c
[ 6%] Built target vectorclass
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color="
[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp
[ 8%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c
[ 8%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 8%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c
[ 8%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c
[ 9%] Building C object booster/CMakeFiles/booster.dir/io.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c
[ 10%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT':
/build/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT':
/build/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp
[ 10%] Building C object booster/CMakeFiles/booster.dir/sort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 10%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c
[ 10%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c
[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 11%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c
[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp
[ 12%] Linking C static library libsprng.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1
/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o
/usr/bin/ranlib libsprng.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 12%] Built target sprng
make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 13%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp
[ 13%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c
[ 14%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c
[ 15%] Linking CXX static library libgsl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA':
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 15%] Built target gsl
[ 16%] Building C object booster/CMakeFiles/booster.dir/booster.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c
[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp
/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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);
| ~~~~~~^~~~~~~~
[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp
[ 17%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c
[ 17%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c
[ 18%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c
[ 18%] Linking CXX static library liblbfgsb.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake
[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu':
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1
[ 20%] Building C object booster/CMakeFiles/booster.dir/prng.c.o
[ 20%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c
/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
/usr/bin/ranlib liblbfgsb.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 20%] Built target lbfgsb
make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color="
[ 20%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
[ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 22%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp
[ 23%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c
[ 24%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp
[ 24%] Building C object booster/CMakeFiles/booster.dir/stats.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c
[ 24%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c
[ 25%] Building C object pll/CMakeFiles/pll.dir/models.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c
[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp
[ 25%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp
[ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp
[ 26%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData':
[ 26%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
/build/reproducible-path/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++/14/bits/stl_function.h:1435:
/usr/include/c++/14/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
[ 27%] Linking C static library libbooster.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 27%] Built target booster
[ 27%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 28%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp
[ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp
[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp
[ 28%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
[ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp
[ 29%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c
[ 29%] Linking CXX static library libwhtest.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
/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
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV':
/build/reproducible-path/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/reproducible-path/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));
| ^~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 29%] Built target whtest
[ 29%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp
[ 30%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp
[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 30%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp
[ 32%] Linking CXX static library libnclextra.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1
/usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o
/usr/bin/ranlib libnclextra.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 32%] Built target nclextra
make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 33%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c
[ 33%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp
[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43:
/build/reproducible-path/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 CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp
[ 35%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 35%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp
[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp
[ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp
[ 36%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp
[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp
[ 37%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42:
/build/reproducible-path/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 C object pll/CMakeFiles/pll.dir/queue.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c
[ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: 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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/map:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 38%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 39%] Building C object pll/CMakeFiles/pll.dir/recom.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c
[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp
[ 41%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp
[ 41%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c
[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47:
/build/reproducible-path/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/multitree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp
[ 42%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c
[ 42%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51:
/build/reproducible-path/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/stack.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c
[ 43%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp
[ 43%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp
[ 44%] Building C object pll/CMakeFiles/pll.dir/trash.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c
[ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 46%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 46%] Building C object pll/CMakeFiles/pll.dir/utils.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c
[ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro 'rax_posix_memalign'
748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) *
| ^~~~~~~~~~~~~~~~~~
[ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp
[ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp
[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o
[ 47%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp
[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp
[ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp
[ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp
[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp
[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp
[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp
[ 52%] Linking C static library libpll.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1
[ 53%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp
/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 53%] Built target pll
[ 53%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp
[ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp
[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp
[ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp
[ 55%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp
[ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp
[ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp
[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp
[ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp
[ 57%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp
[ 58%] Linking CXX static library libutils.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1
[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp
[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp
[ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 59%] Built target utils
make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 59%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 60%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 62%] Linking CXX static library libterraphast.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake
[ 62%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1
/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o
/usr/bin/ranlib libterraphast.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 62%] Built target terraphast
[ 62%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp
[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp
[ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 64%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 64%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 65%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp
[ 65%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp
[ 65%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c
[ 65%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp
[ 67%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 68%] Linking CXX static library libyaml-cpp.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1
/usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o"
/usr/bin/ranlib libyaml-cpp.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 68%] Built target yaml-cpp
make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 68%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp
[ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp
[ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 69%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp
[ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp
[ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 70%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30:
/build/reproducible-path/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);
| ^~~~~
[ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp
[ 72%] Linking CXX static library libncl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 72%] Built target ncl
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build
/build/reproducible-path/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);
| ^~~~~
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
892 | void ModelProtein::readRates(istream &in) throw(const char*, string) {
| ^~~~~
[ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp
[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /usr/include/boost/math/distributions/binomial.hpp:83,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp
[ 73%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp
[ 74%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 74%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 75%] Linking CXX static library libpda.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1
[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp
/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
/usr/bin/ranlib libpda.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 76%] Built target pda
make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 77%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp
[ 77%] Linking CXX static library libphyloYAML.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 77%] Built target phyloYAML
[ 77%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp
/build/reproducible-path/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__;
| ^~~~~~~~
[ 77%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp
/build/reproducible-path/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
| ^~~~~~~~
[ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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) {
| ^~~~~
[ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 79%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp
[ 81%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp
[ 82%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 82%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13:
/build/reproducible-path/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);
| ^~~~~
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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 model/CMakeFiles/model.dir/modelpomo.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /usr/include/c++/14/complex:45,
from /usr/include/eigen3/Eigen/Core:50,
from /usr/include/eigen3/Eigen/Dense:1,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 84%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp
[ 84%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp
[ 84%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 85%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp
[ 85%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34:
/build/reproducible-path/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);
| ^~~~~
[ 86%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type]
180 | }
| ^
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type]
257 | }
| ^
[ 86%] 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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 86%] Built target kernelsse
[ 87%] Linking CXX static library libmain.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
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[ 87%] Built target main
[ 87%] Linking CXX static library libalignment.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
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[ 87%] Built target alignment
[ 88%] Linking CXX static library libmodel.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
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[ 88%] Built target model
make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color="
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make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build
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[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp
[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type]
653 | }
| ^
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp
[ 97%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp
[ 98%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 98%] Linking CXX static library libtree.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[100%] Linking CXX static library libterrace.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[100%] Built target terrace
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib32 -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib32: 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 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/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
[100%] Built target iqtree2
make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
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# 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 -j11 "INSTALL=install --strip-program=true" VERBOSE=1
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/usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color="
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake "--color="
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[ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c
make[4]: Entering directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
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/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp
[ 4%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
[ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c
[ 5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c
[ 5%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp
[ 5%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c:40:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
[ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp
[ 7%] Linking CXX static library libvectorclass.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1
[ 7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c
[ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
/usr/bin/ranlib libvectorclass.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp
[ 8%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c
[ 8%] Built target vectorclass
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 8%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c
[ 8%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c
[ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c
[ 9%] Building C object booster/CMakeFiles/booster.dir/io.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c
[ 10%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c
[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function 'insertHashRF':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro 'rax_posix_memalign'
332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int));
| ^~~~~~~~~~~~~~~~~~
[ 10%] Building C object booster/CMakeFiles/booster.dir/sort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c
[ 10%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c
[ 10%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 11%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c
[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp
[ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
| ^~~~~~~~~~~~~~~
[ 13%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c
[ 13%] Linking C static library libsprng.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 13%] Built target sprng
make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 14%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp
[ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp
[ 15%] Linking CXX static library libgsl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1
/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o
/usr/bin/ranlib libgsl.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 15%] Built target gsl
[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp
[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
/build/reproducible-path/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++/14/bits/stl_function.h:1435:
/usr/include/c++/14/backward/binders.h:172:5: note: declared here
172 | bind2nd(const _Operation& __fn, const _Tp& __x)
| ^~~~~~~
[ 17%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c
[ 17%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp
[ 17%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp
[ 18%] Building C object booster/CMakeFiles/booster.dir/booster.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c
[ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c
/build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c:27:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCAT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMA':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRCATPROT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function 'evaluatePartialGTRGAMMAPROT':
/build/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
[ 18%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c
[ 18%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c
[ 19%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o
[ 20%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c
[ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp
[ 21%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c
[ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c
[ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function 'compressDNA':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~
[ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c
[ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp
[ 22%] Building C object booster/CMakeFiles/booster.dir/stats.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Linking CXX static library liblbfgsb.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 22%] Built target lbfgsb
make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color="
[ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 23%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c
[ 24%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp
/build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function 'ReadData':
/build/reproducible-path/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/reproducible-path/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 );
| ^~~~~~~~~~~~~~~~~~~~~~~~
[ 24%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c
[ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp
[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp
[ 27%] Linking C static library libbooster.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o
/usr/bin/ranlib libbooster.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp
[ 28%] Built target booster
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp
[ 29%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu':
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~~~~~~~~
[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp
[ 30%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 30%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp
[ 31%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 31%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT':
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign'
3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double));
| ^~~~~~~~~~~~~~~~~~
[ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp
[ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp
[ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp
[ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp
[ 33%] Linking CXX static library libwhtest.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 33%] Built target whtest
[ 33%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp
[ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp
[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 35%] Building C object pll/CMakeFiles/pll.dir/models.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c
[ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp
[ 35%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53:
/build/reproducible-path/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 CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp
[ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp
[ 36%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp
[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp
[ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp
[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp
[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp
[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -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/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp
[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp
[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 42%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c
[ 42%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp
[ 42%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 43%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllNewviewIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'pllGetCLV':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 43%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp
[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp
[ 44%] Linking CXX static library libnclextra.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 44%] Built target nclextra
make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 44%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp
[ 45%] Linking CXX static library libterraphast.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/map:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1
[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp
[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 46%] Built target terraphast
[ 47%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp
[ 47%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47:
/build/reproducible-path/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 CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp
[ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp
[ 49%] Linking CXX static library libncl.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 49%] Built target ncl
[ 50%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp
[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 51%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp
[ 52%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 52%] Building C object pll/CMakeFiles/pll.dir/queue.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c
[ 52%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c
[ 53%] Building C object pll/CMakeFiles/pll.dir/recom.c.o
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c
[ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp
[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp
[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp
[ 55%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o
[ 55%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c:43:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c
[ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 56%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c
[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp
[ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp
[ 57%] Building C object pll/CMakeFiles/pll.dir/stack.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c
[ 57%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c:48:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 58%] Building C object pll/CMakeFiles/pll.dir/trash.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c
[ 59%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c:48:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 59%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.c:49:
/build/reproducible-path/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);
| ^~~~~~~~~~~~~~~
[ 60%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp
[ 60%] Building C object pll/CMakeFiles/pll.dir/utils.c.o
[ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp
[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c:70:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:16:
/build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c: In function 'initializePartitionData':
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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) *
| ^~~~~~~~~~~~~~~~~~
[ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp
[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c
[ 63%] Linking C static library libpll.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake
[ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp
[ 64%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1
/usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o
/usr/bin/ranlib libpll.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 64%] Built target pll
make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp
[ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/fstream:40,
from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp
[ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp
[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp
[ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
from /usr/include/boost/math/special_functions/beta.hpp:13,
from /usr/include/boost/math/distributions/binomial.hpp:83,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22:
/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
| ^~~~~~~
[ 67%] Linking CXX static library libutils.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 67%] Built target utils
make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 67%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp
[ 67%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
[ 68%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp
[ 68%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -std=gnu++11 -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -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/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 68%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp
[ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp
[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp
[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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) {
| ^~~~~
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
242 | void ModelDNA::readRates(string str) throw(const char*) {
| ^~~~~
[ 72%] Linking CXX static library libyaml-cpp.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30:
/build/reproducible-path/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);
| ^~~~~
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 72%] Built target yaml-cpp
make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 72%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp
[ 72%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
892 | void ModelProtein::readRates(istream &in) throw(const char*, string) {
| ^~~~~
[ 73%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp
[ 74%] Linking CXX static library libpda.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake "--color="
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 75%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 75%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/ostream:40,
from /usr/include/c++/14/iostream:41,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
167 | virtual void readStateFreq(string str) throw(const char*);
| ^~~~~
[ 76%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp
[ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 76%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 77%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp
[ 78%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
[ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 79%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp
[ 79%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp
[ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp
/build/reproducible-path/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
| ^~~~~~~~
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp
[ 80%] Linking CXX static library libphyloYAML.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp
[ 80%] Built target phyloYAML
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
/build/reproducible-path/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);
| ^~~~~
[ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 82%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp
[ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function 'std::string getSeqTypeName(PML::SeqType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type]
180 | }
| ^
[ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)':
/build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type]
257 | }
| ^
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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) {
| ^~~~~
[ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp
[ 85%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10:
/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp
[ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp
[ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/string:49,
from /usr/include/c++/14/bits/locale_classes.h:40,
from /usr/include/c++/14/bits/ios_base.h:41,
from /usr/include/c++/14/ios:44,
from /usr/include/c++/14/istream:40,
from /usr/include/c++/14/sstream:40,
from /usr/include/c++/14/complex:45,
from /usr/include/eigen3/Eigen/Core:50,
from /usr/include/eigen3/Eigen/Dense:1,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 86%] 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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 86%] Built target kernelsse
[ 86%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 87%] Linking CXX static library libmain.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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
/usr/bin/ranlib libmain.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 87%] Built target main
[ 87%] Linking CXX static library libalignment.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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 libalignment.a
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 87%] Built target alignment
[ 88%] Linking CXX static library libmodel.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 88%] Built target model
make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake "--color="
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[ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp
[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp
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cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp
[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp
[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp
[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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*);
| ^~~~~
[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp
[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp
[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35:
/build/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function 'std::string getASCName(ASCType)':
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type]
653 | }
| ^
/build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)':
/build/reproducible-path/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/quartet.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp
[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 97%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp
[ 98%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/stl_tree.h:65,
from /usr/include/c++/14/set:62,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 98%] Linking CXX static library libtree.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.h:27,
from /build/reproducible-path/iqtree-2.0.7+dfsg/terrace/terrace.cpp:20:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[100%] Linking CXX static library libterrace.a
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake
cd /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[100%] Built target terrace
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake "--color="
make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build
make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o
/usr/bin/c++ -DBINARY32 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/i386-linux-gnu/mpich/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/include -I/build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -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/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp
In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
from /build/reproducible-path/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp:21:
/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
172 | : public binary_function<NxsString, NxsString, bool>
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/bits/refwrap.h:39,
from /usr/include/c++/14/vector:68,
from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
/usr/include/c++/14/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/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -m32 -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic -Wl,--dependency-file=CMakeFiles/iqtree2.dir/link.d CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib32 -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib32:/usr/lib/i386-linux-gnu/mpich/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/i386-linux-gnu/mpich/lib/libmpichcxx.so /usr/lib/i386-linux-gnu/mpich/lib/libmpich.so 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/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
[100%] Built target iqtree2
make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles 0
make[2]: Leaving directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short
time sh example.short
Executing tests using /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ...
+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy
IQ-TREE multicore version 2.0.7 for Linux 32-bit built Jan 21 2022
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: ionos2-i386 (SSE4.2, 7 GB RAM)
Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy
Seed: 542704 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Feb 27 23:25:30 2025
Kernel: SSE2 - 1 threads (13 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 13 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 17 sequences with 1998 columns, 1152 distinct patterns
1009 parsimony-informative, 303 singleton sites, 685 constant sites
Gap/Ambiguity Composition p-value
1 LngfishAu 0.15% passed 6.20%
2 LngfishSA 0.00% failed 0.62%
3 LngfishAf 0.05% failed 1.60%
4 Frog 0.05% passed 58.01%
5 Turtle 0.15% passed 44.25%
6 Sphenodon 0.10% passed 59.78%
7 Lizard 0.90% passed 38.67%
8 Crocodile 0.35% failed 2.51%
9 Bird 0.00% failed 0.00%
10 Human 0.00% failed 0.85%
11 Seal 0.00% passed 68.93%
12 Cow 0.00% passed 59.11%
13 Whale 0.00% passed 97.83%
14 Mouse 0.05% failed 1.43%
15 Rat 0.00% passed 39.69%
16 Platypus 0.00% failed 3.46%
17 Opossum 0.00% failed 0.01%
**** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -21149.228
Optimal log-likelihood: -21149.102
Rate parameters: A-C: 3.72817 A-G: 5.18875 A-T: 3.86003 C-G: 0.42102 C-T: 15.28308 G-T: 1.00000
Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225
Proportion of invariable sites: 0.157
Gamma shape alpha: 0.740
Parameters optimization took 1 rounds (0.098 sec)
Time for fast ML tree search: 1.136 seconds
NOTE: ModelFinder requires 6 MB RAM!
ModelFinder will test up to 286 DNA models (sample size: 1998) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 22701.469 39 45480.937 45482.531 45699.334
2 GTR+F+I 21615.548 40 43311.095 43312.772 43535.092
3 GTR+F+G4 21155.969 40 42391.939 42393.615 42615.935
4 GTR+F+I+G4 21148.848 41 42379.696 42381.457 42609.292
5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922
6 GTR+F+R3 21147.208 43 42380.415 42382.352 42621.211
7 GTR+F+R4 21145.838 45 42381.676 42383.797 42633.672
16 SYM+G4 21317.781 37 42709.562 42710.997 42916.758
17 SYM+I+G4 21306.169 38 42688.337 42689.850 42901.133
29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870
30 TVM+F+I+G4 21288.268 40 42656.537 42658.213 42880.533
42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969
43 TVMe+I+G4 21407.599 37 42889.197 42890.632 43096.393
55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649
56 TIM3+F+I+G4 21359.482 39 42796.964 42798.557 43015.360
68 TIM3e+G4 21717.462 35 43504.924 43506.208 43700.920
69 TIM3e+I+G4 21708.558 36 43489.116 43490.475 43690.713
81 TIM2+F+G4 21159.705 38 42395.410 42396.923 42608.206
82 TIM2+F+I+G4 21152.488 39 42382.975 42384.569 42601.372
94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757
95 TIM2e+I+G4 21309.125 36 42690.251 42691.609 42891.847
107 TIM+F+G4 21368.782 38 42813.565 42815.078 43026.361
108 TIM+F+I+G4 21360.236 39 42798.472 42800.065 43016.868
120 TIMe+G4 21718.131 35 43506.263 43507.547 43702.259
121 TIMe+I+G4 21709.219 36 43490.437 43491.796 43692.034
133 TPM3u+F+G4 21488.893 37 43051.785 43053.220 43258.982
134 TPM3u+F+I+G4 21474.932 38 43025.864 43027.377 43238.661
146 TPM3+F+G4 21488.893 37 43051.785 43053.220 43258.982
147 TPM3+F+I+G4 21474.932 38 43025.864 43027.377 43238.661
159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.791
160 TPM2u+F+I+G4 21291.864 38 42659.727 42661.240 42872.523
172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.791
173 TPM2+F+I+G4 21291.864 38 42659.727 42661.240 42872.523
185 K3Pu+F+G4 21489.348 37 43052.696 43054.130 43259.892
186 K3Pu+F+I+G4 21475.428 38 43026.855 43028.368 43239.652
198 K3P+G4 21847.491 34 43762.981 43764.193 43953.378
199 K3P+I+G4 21833.792 35 43737.583 43738.868 43933.580
211 TN+F+G4 21369.048 37 42812.096 42813.531 43019.292
212 TN+F+I+G4 21360.517 38 42797.035 42798.548 43009.831
224 TNe+G4 21718.202 34 43504.403 43505.616 43694.800
225 TNe+I+G4 21709.279 35 43488.557 43489.842 43684.554
237 HKY+F+G4 21489.737 36 43051.474 43052.833 43253.071
238 HKY+F+I+G4 21475.765 37 43025.530 43026.965 43232.726
250 K2P+G4 21847.675 33 43761.349 43762.492 43946.146
251 K2P+I+G4 21833.945 34 43735.890 43737.102 43926.287
263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152
264 F81+F+I+G4 22019.571 36 44111.141 44112.500 44312.738
276 JC+G4 22258.086 32 44580.172 44581.246 44759.368
277 JC+I+G4 22245.551 33 44557.101 44558.244 44741.898
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: TIM2+F+I+G4
Best-fit model: TIM2+F+I+G4 chosen according to BIC
All model information printed to example.phy.model.gz
CPU time for ModelFinder: 17.814 seconds (0h:0m:17s)
Wall-clock time for ModelFinder: 18.257 seconds (0h:0m:18s)
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, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748
Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.977
Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.641
Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.215
Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.514
Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778
Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833
Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.863
Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876
Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.903
Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514
Parameters optimization took 4.637 sec
Computing ML distances based on estimated model parameters... 0.015 sec
Computing BIONJ tree...
0.001 seconds
Log-likelihood of BIONJ tree: -21157.742
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.660 second
Computing log-likelihood of 98 initial trees ... 1.693 seconds
Current best score: -21152.514
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -21152.510
Iteration 10 / LogL: -21152.528 / Time: 0h:0m:8s
Iteration 20 / LogL: -21152.568 / Time: 0h:0m:11s
Finish initializing candidate tree set (2)
Current best tree score: -21152.510 / CPU time: 6.422
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Iteration 30 / LogL: -21152.566 / Time: 0h:0m:13s (0h:0m:33s left)
Iteration 40 / LogL: -21157.987 / Time: 0h:0m:15s (0h:0m:24s left)
Iteration 50 / LogL: -21152.594 / Time: 0h:0m:18s (0h:0m:18s left)
Iteration 60 / LogL: -21152.792 / Time: 0h:0m:20s (0h:0m:14s left)
Iteration 70 / LogL: -21158.664 / Time: 0h:0m:22s (0h:0m:10s left)
Iteration 80 / LogL: -21152.717 / Time: 0h:0m:24s (0h:0m:6s left)
Iteration 90 / LogL: -21153.389 / Time: 0h:0m:27s (0h:0m:3s left)
Iteration 100 / LogL: -21152.515 / Time: 0h:0m:29s (0h:0m:0s left)
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:30s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -21152.510
Optimal log-likelihood: -21152.506
Rate parameters: A-C: 5.71185 A-G: 7.80633 A-T: 5.71185 C-G: 1.00000 C-T: 23.18055 G-T: 1.00000
Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225
Proportion of invariable sites: 0.154
Gamma shape alpha: 0.728
Parameters optimization took 1 rounds (0.056 sec)
BEST SCORE FOUND : -21152.506
Total tree length: 4.226
Total number of iterations: 102
CPU time used for tree search: 24.427 sec (0h:0m:24s)
Wall-clock time used for tree search: 25.392 sec (0h:0m:25s)
Total CPU time used: 29.122 sec (0h:0m:29s)
Total wall-clock time used: 30.186 sec (0h:0m:30s)
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: Thu Feb 27 23:26:19 2025
46.95user 1.46system 0:48.50elapsed 99%CPU (0avgtext+0avgdata 13488maxresident)k
7816inputs+136outputs (55major+31714minor)pagefaults 0swaps
+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo
IQ-TREE multicore version 2.0.7 for Linux 32-bit built Jan 21 2022
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Host: ionos2-i386 (SSE4.2, 7 GB RAM)
Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo
Seed: 30487 (Using SPRNG - Scalable Parallel Random Number Generator)
Time: Thu Feb 27 23:26:19 2025
Kernel: SSE2 - 1 threads (13 CPU cores detected)
HINT: Use -nt option to specify number of threads because your CPU has 13 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 17 sequences with 1998 columns, 1152 distinct patterns
1009 parsimony-informative, 303 singleton sites, 685 constant sites
Gap/Ambiguity Composition p-value
1 LngfishAu 0.15% passed 6.20%
2 LngfishSA 0.00% failed 0.62%
3 LngfishAf 0.05% failed 1.60%
4 Frog 0.05% passed 58.01%
5 Turtle 0.15% passed 44.25%
6 Sphenodon 0.10% passed 59.78%
7 Lizard 0.90% passed 38.67%
8 Crocodile 0.35% failed 2.51%
9 Bird 0.00% failed 0.00%
10 Human 0.00% failed 0.85%
11 Seal 0.00% passed 68.93%
12 Cow 0.00% passed 59.11%
13 Whale 0.00% passed 97.83%
14 Mouse 0.05% failed 1.43%
15 Rat 0.00% passed 39.69%
16 Platypus 0.00% failed 3.46%
17 Opossum 0.00% failed 0.01%
**** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3)
Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.006 seconds
Perform fast likelihood tree search using GTR+I+G model...
Estimate model parameters (epsilon = 5.000)
Perform nearest neighbor interchange...
Estimate model parameters (epsilon = 1.000)
1. Initial log-likelihood: -21149.228
Optimal log-likelihood: -21149.102
Rate parameters: A-C: 3.72817 A-G: 5.18875 A-T: 3.86003 C-G: 0.42102 C-T: 15.28308 G-T: 1.00000
Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225
Proportion of invariable sites: 0.157
Gamma shape alpha: 0.740
Parameters optimization took 1 rounds (0.100 sec)
Time for fast ML tree search: 1.132 seconds
NOTE: ModelFinder requires 6 MB RAM!
ModelFinder will test up to 286 DNA models (sample size: 1998) ...
No. Model -LnL df AIC AICc BIC
1 GTR+F 22701.469 39 45480.937 45482.531 45699.334
2 GTR+F+I 21615.548 40 43311.095 43312.772 43535.092
3 GTR+F+G4 21155.969 40 42391.939 42393.615 42615.935
4 GTR+F+I+G4 21148.848 41 42379.696 42381.457 42609.292
5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922
6 GTR+F+R3 21147.208 43 42380.415 42382.352 42621.211
7 GTR+F+R4 21145.838 45 42381.676 42383.797 42633.672
16 SYM+G4 21317.781 37 42709.562 42710.997 42916.758
17 SYM+I+G4 21306.169 38 42688.337 42689.850 42901.133
29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870
30 TVM+F+I+G4 21288.268 40 42656.537 42658.213 42880.533
42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969
43 TVMe+I+G4 21407.599 37 42889.197 42890.632 43096.393
55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649
56 TIM3+F+I+G4 21359.482 39 42796.964 42798.557 43015.360
68 TIM3e+G4 21717.462 35 43504.924 43506.208 43700.920
69 TIM3e+I+G4 21708.558 36 43489.116 43490.475 43690.713
81 TIM2+F+G4 21159.705 38 42395.410 42396.923 42608.206
82 TIM2+F+I+G4 21152.488 39 42382.975 42384.569 42601.372
94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757
95 TIM2e+I+G4 21309.125 36 42690.251 42691.609 42891.847
107 TIM+F+G4 21368.782 38 42813.565 42815.078 43026.361
108 TIM+F+I+G4 21360.236 39 42798.472 42800.065 43016.868
120 TIMe+G4 21718.131 35 43506.263 43507.547 43702.259
121 TIMe+I+G4 21709.219 36 43490.437 43491.796 43692.034
133 TPM3u+F+G4 21488.893 37 43051.785 43053.220 43258.982
134 TPM3u+F+I+G4 21474.932 38 43025.864 43027.377 43238.661
146 TPM3+F+G4 21488.893 37 43051.785 43053.220 43258.982
147 TPM3+F+I+G4 21474.932 38 43025.864 43027.377 43238.661
159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.791
160 TPM2u+F+I+G4 21291.864 38 42659.727 42661.240 42872.523
172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.791
173 TPM2+F+I+G4 21291.864 38 42659.727 42661.240 42872.523
185 K3Pu+F+G4 21489.348 37 43052.696 43054.130 43259.892
186 K3Pu+F+I+G4 21475.428 38 43026.855 43028.368 43239.652
198 K3P+G4 21847.491 34 43762.981 43764.193 43953.378
199 K3P+I+G4 21833.792 35 43737.583 43738.868 43933.580
211 TN+F+G4 21369.048 37 42812.096 42813.531 43019.292
212 TN+F+I+G4 21360.517 38 42797.035 42798.548 43009.831
224 TNe+G4 21718.202 34 43504.403 43505.616 43694.800
225 TNe+I+G4 21709.279 35 43488.557 43489.842 43684.554
237 HKY+F+G4 21489.737 36 43051.474 43052.833 43253.071
238 HKY+F+I+G4 21475.765 37 43025.530 43026.965 43232.726
250 K2P+G4 21847.675 33 43761.349 43762.492 43946.146
251 K2P+I+G4 21833.945 34 43735.890 43737.102 43926.287
263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152
264 F81+F+I+G4 22019.571 36 44111.141 44112.500 44312.738
276 JC+G4 22258.086 32 44580.172 44581.246 44759.368
277 JC+I+G4 22245.551 33 44557.101 44558.244 44741.898
Akaike Information Criterion: GTR+F+I+G4
Corrected Akaike Information Criterion: GTR+F+I+G4
Bayesian Information Criterion: TIM2+F+I+G4
Best-fit model: TIM2+F+I+G4 chosen according to BIC
All model information printed to example.phy.model.gz
CPU time for ModelFinder: 17.788 seconds (0h:0m:17s)
Wall-clock time for ModelFinder: 18.851 seconds (0h:0m:18s)
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, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748
Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.977
Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.641
Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.215
Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.514
Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778
Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833
Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.863
Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876
Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.903
Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514
Parameters optimization took 5.081 sec
Computing ML distances based on estimated model parameters... 0.016 sec
Computing BIONJ tree...
0.001 seconds
Log-likelihood of BIONJ tree: -21157.742
--------------------------------------------------------------------
| INITIALIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Generating 98 parsimony trees... 0.645 second
Computing log-likelihood of 98 initial trees ... 1.671 seconds
Current best score: -21152.514
Do NNI search on 20 best initial trees
Estimate model parameters (epsilon = 0.100)
BETTER TREE FOUND at iteration 1: -21152.510
Iteration 10 / LogL: -21152.559 / Time: 0h:0m:9s
Iteration 20 / LogL: -21157.821 / Time: 0h:0m:11s
Finish initializing candidate tree set (2)
Current best tree score: -21152.510 / CPU time: 6.392
Number of iterations: 20
--------------------------------------------------------------------
| OPTIMIZING CANDIDATE TREE SET |
--------------------------------------------------------------------
Iteration 30 / LogL: -21152.527 / Time: 0h:0m:13s (0h:0m:34s left)
Iteration 40 / LogL: -21152.537 / Time: 0h:0m:16s (0h:0m:25s left)
Iteration 50 / LogL: -21152.522 / Time: 0h:0m:18s (0h:0m:19s left)
Iteration 60 / LogL: -21152.518 / Time: 0h:0m:21s (0h:0m:14s left)
Iteration 70 / LogL: -21152.541 / Time: 0h:0m:23s (0h:0m:10s left)
Iteration 80 / LogL: -21152.819 / Time: 0h:0m:25s (0h:0m:6s left)
Iteration 90 / LogL: -21152.604 / Time: 0h:0m:27s (0h:0m:3s left)
Iteration 100 / LogL: -21153.066 / Time: 0h:0m:30s (0h:0m:0s left)
TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:30s
--------------------------------------------------------------------
| FINALIZING TREE SEARCH |
--------------------------------------------------------------------
Performs final model parameters optimization
Estimate model parameters (epsilon = 0.010)
1. Initial log-likelihood: -21152.510
Optimal log-likelihood: -21152.506
Rate parameters: A-C: 5.71185 A-G: 7.80633 A-T: 5.71185 C-G: 1.00000 C-T: 23.18055 G-T: 1.00000
Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225
Proportion of invariable sites: 0.154
Gamma shape alpha: 0.728
Parameters optimization took 1 rounds (0.057 sec)
BEST SCORE FOUND : -21152.506
Total tree length: 4.226
Total number of iterations: 102
CPU time used for tree search: 24.478 sec (0h:0m:24s)
Wall-clock time used for tree search: 25.551 sec (0h:0m:25s)
Total CPU time used: 29.301 sec (0h:0m:29s)
Total wall-clock time used: 30.790 sec (0h:0m:30s)
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: Thu Feb 27 23:27:08 2025
47.09user 1.61system 0:49.66elapsed 98%CPU (0avgtext+0avgdata 13284maxresident)k
16inputs+184outputs (1major+31753minor)pagefaults 0swaps
+ rm -rf /tmp/iqtree-test.tPK2u2
94.09user 3.13system 1:38.30elapsed 98%CPU (0avgtext+0avgdata 13488maxresident)k
9976inputs+400outputs (74major+64851minor)pagefaults 0swaps
rm example.short
make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/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 -j11 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
/usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2" to ""
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf
make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi
cd build.mpi && make -j11 install DESTDIR=/build/reproducible-path/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
/usr/bin/cmake -S/build/reproducible-path/iqtree-2.0.7+dfsg -B/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
make[3]: Nothing to be done for 'preinstall'.
make[3]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi
-- Set non-toolchain portion of runtime path of "/build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to ""
-- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex
-- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy
-- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex
-- Up-to-date: /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf
make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
dh override_dh_auto_install
make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
debian/rules override_dh_install
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg'
dh_installdocs
dh_installchangelogs
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg'
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
mkdir -p /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/reproducible-path/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/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/reproducible-path/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1
make[1]: Leaving directory '/build/reproducible-path/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_i386.deb'.
dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1_i386.deb'.
dpkg-genbuildinfo --build=binary -O../iqtree_2.0.7+dfsg-1_i386.buildinfo
dpkg-genchanges --build=binary -O../iqtree_2.0.7+dfsg-1_i386.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/30737 and its subdirectories
I: Current time: Thu Feb 27 11:29:50 -12 2025
I: pbuilder-time-stamp: 1740698990