I: pbuilder: network access will be disabled during build I: Current time: Sat Jun 8 08:48:14 +14 2024 I: pbuilder-time-stamp: 1717786094 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: Copying source file I: copying [iqtree_2.0.7+dfsg-1.dsc] I: copying [./iqtree_2.0.7+dfsg.orig.tar.xz] I: copying [./iqtree_2.0.7+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 21 14:08:08 2022 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./iqtree_2.0.7+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting iqtree in iqtree-2.0.7+dfsg dpkg-source: info: unpacking iqtree_2.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Jun 7 18:48 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=f8b15321e201425187b7bc68d453727e LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2616740 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.QsQz2ngd/pbuilderrc_W32H --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.QsQz2ngd/b2 --logfile b2/build.log iqtree_2.0.7+dfsg-1.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 5 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19701 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-13{a} gfortran-13-x86-64-linux-gnu{a} groff-base{a} help2man{a} ibverbs-providers{a} intltool-debian{a} libamd-comgr2{a} libamdhip64-5{a} libarchive-zip-perl{a} libarchive13t64{a} libboost-dev{a} libboost1.83-dev{a} libbrotli1{a} libbsd0{a} libcbor0.10{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm2{a} libedit2{a} libeigen3-dev{a} libelf1t64{a} libevent-2.1-7t64{a} libevent-core-2.1-7t64{a} libevent-dev{a} libevent-extra-2.1-7t64{a} libevent-openssl-2.1-7t64{a} libevent-pthreads-2.1-7t64{a} libexpat1{a} libfabric1{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libgfortran-13-dev{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgssapi-krb5-2{a} libhsa-runtime64-1{a} libhsakmt1{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libicu72{a} libjs-jquery{a} libjs-jquery-ui{a} libjsoncpp25{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libllvm17t64{a} liblocale-gettext-perl{a} libltdl-dev{a} libltdl7{a} libmagic-mgc{a} libmagic1t64{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenmpi-dev{a} libopenmpi3t64{a} libpciaccess0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libproc2-0{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} librdmacm1t64{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsprng2{a} libsprng2-dev{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libucx0{a} libuv1t64{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxnvctrl0{a} libz3-4{a} m4{a} man-db{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} time{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common krb5-locales libarchive-cpio-perl libcoarrays-openmpi-dev libldap-common libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget xauth 0 packages upgraded, 131 newly installed, 0 to remove and 0 not upgraded. Need to get 133 MB of archives. After unpacking 657 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main amd64 liblocale-gettext-perl amd64 1.07-7 [15.0 kB] Get: 2 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get: 3 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get: 4 http://deb.debian.org/debian trixie/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get: 5 http://deb.debian.org/debian trixie/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get: 6 http://deb.debian.org/debian trixie/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get: 7 http://deb.debian.org/debian trixie/main amd64 file amd64 1:5.45-3 [42.9 kB] Get: 8 http://deb.debian.org/debian trixie/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get: 9 http://deb.debian.org/debian trixie/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get: 10 http://deb.debian.org/debian trixie/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get: 11 http://deb.debian.org/debian trixie/main amd64 bsdextrautils amd64 2.40.1-8 [96.0 kB] Get: 12 http://deb.debian.org/debian trixie/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get: 13 http://deb.debian.org/debian trixie/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get: 14 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get: 15 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240517-1 [93.3 kB] Get: 16 http://deb.debian.org/debian trixie/main amd64 libcbor0.10 amd64 0.10.2-1.1 [27.8 kB] Get: 17 http://deb.debian.org/debian trixie/main amd64 libfido2-1 amd64 1.14.0-1+b2 [77.7 kB] Get: 18 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get: 19 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get: 20 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get: 21 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get: 22 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get: 23 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get: 24 http://deb.debian.org/debian trixie/main amd64 openssh-client amd64 1:9.7p1-5 [964 kB] Get: 25 http://deb.debian.org/debian trixie/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 26 http://deb.debian.org/debian trixie/main amd64 autoconf all 2.71-3 [332 kB] Get: 27 http://deb.debian.org/debian trixie/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian trixie/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian trixie/main amd64 autopoint all 0.21-14 [496 kB] Get: 30 http://deb.debian.org/debian trixie/main amd64 chrpath amd64 0.16-2+b1 [17.1 kB] Get: 31 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get: 32 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b3 [692 kB] Get: 33 http://deb.debian.org/debian trixie/main amd64 libarchive13t64 amd64 3.7.2-2.1 [346 kB] Get: 34 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get: 35 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get: 36 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get: 37 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.17+dfsg-1 [186 kB] Get: 38 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.61.0-1+b1 [75.6 kB] Get: 39 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get: 40 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get: 41 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.0-5 [215 kB] Get: 42 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.8.0-1 [441 kB] Get: 43 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get: 44 http://deb.debian.org/debian trixie/main amd64 libjsoncpp25 amd64 1.9.5-6+b2 [81.9 kB] Get: 45 http://deb.debian.org/debian trixie/main amd64 librhash0 amd64 1.4.3-3+b1 [132 kB] Get: 46 http://deb.debian.org/debian trixie/main amd64 libuv1t64 amd64 1.48.0-4 [148 kB] Get: 47 http://deb.debian.org/debian trixie/main amd64 cmake-data all 3.29.4-1 [2167 kB] Get: 48 http://deb.debian.org/debian trixie/main amd64 cmake amd64 3.29.4-1 [10.7 MB] Get: 49 http://deb.debian.org/debian trixie/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 50 http://deb.debian.org/debian trixie/main amd64 libtool all 2.4.7-7 [517 kB] Get: 51 http://deb.debian.org/debian trixie/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 55 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get: 56 http://deb.debian.org/debian trixie/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 57 http://deb.debian.org/debian trixie/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get: 58 http://deb.debian.org/debian trixie/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 61 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get: 62 http://deb.debian.org/debian trixie/main amd64 libgfortran-13-dev amd64 13.2.0-25 [847 kB] Get: 63 http://deb.debian.org/debian trixie/main amd64 gfortran-13-x86-64-linux-gnu amd64 13.2.0-25 [10.6 MB] Get: 64 http://deb.debian.org/debian trixie/main amd64 gfortran-13 amd64 13.2.0-25 [12.8 kB] Get: 65 http://deb.debian.org/debian trixie/main amd64 help2man amd64 1.49.3 [198 kB] Get: 66 http://deb.debian.org/debian trixie/main amd64 libnl-3-200 amd64 3.7.0-0.3 [59.0 kB] Get: 67 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-200 amd64 3.7.0-0.3 [181 kB] Get: 68 http://deb.debian.org/debian trixie/main amd64 libibverbs1 amd64 50.0-2+b1 [61.7 kB] Get: 69 http://deb.debian.org/debian trixie/main amd64 ibverbs-providers amd64 50.0-2+b1 [342 kB] Get: 70 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get: 71 http://deb.debian.org/debian trixie/main amd64 libllvm17t64 amd64 1:17.0.6-12 [23.7 MB] Get: 72 http://deb.debian.org/debian trixie/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b1 [13.0 MB] Get: 73 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get: 74 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get: 75 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get: 76 http://deb.debian.org/debian trixie/main amd64 libnuma1 amd64 2.0.18-1 [21.9 kB] Get: 77 http://deb.debian.org/debian trixie/main amd64 libhsakmt1 amd64 5.7.0-1 [60.7 kB] Get: 78 http://deb.debian.org/debian trixie/main amd64 libhsa-runtime64-1 amd64 5.7.1-2 [504 kB] Get: 79 http://deb.debian.org/debian trixie/main amd64 libamdhip64-5 amd64 5.7.1-3 [8760 kB] Get: 80 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3 [10.6 MB] Get: 81 http://deb.debian.org/debian trixie/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 82 http://deb.debian.org/debian trixie/main amd64 libpkgconf3 amd64 1.8.1-1+b2 [36.4 kB] Get: 83 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 84 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 85 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] Get: 86 http://deb.debian.org/debian trixie/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 87 http://deb.debian.org/debian trixie/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10 [181 kB] Get: 88 http://deb.debian.org/debian trixie/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10 [131 kB] Get: 89 http://deb.debian.org/debian trixie/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10 [107 kB] Get: 90 http://deb.debian.org/debian trixie/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10 [53.9 kB] Get: 91 http://deb.debian.org/debian trixie/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10 [60.8 kB] Get: 92 http://deb.debian.org/debian trixie/main amd64 libevent-dev amd64 2.1.12-stable-10 [305 kB] Get: 93 http://deb.debian.org/debian trixie/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 94 http://deb.debian.org/debian trixie/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get: 95 http://deb.debian.org/debian trixie/main amd64 librdmacm1t64 amd64 50.0-2+b1 [70.2 kB] Get: 96 http://deb.debian.org/debian trixie/main amd64 libfabric1 amd64 1.17.0-3+b1 [628 kB] Get: 97 http://deb.debian.org/debian trixie/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-2+b1 [329 kB] Get: 98 http://deb.debian.org/debian trixie/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-2+b1 [640 kB] Get: 99 http://deb.debian.org/debian trixie/main amd64 libhwloc15 amd64 2.10.0-1+b1 [161 kB] Get: 100 http://deb.debian.org/debian trixie/main amd64 libnuma-dev amd64 2.0.18-1 [36.2 kB] Get: 101 http://deb.debian.org/debian trixie/main amd64 libltdl7 amd64 2.4.7-7+b1 [393 kB] Get: 102 http://deb.debian.org/debian trixie/main amd64 libltdl-dev amd64 2.4.7-7+b1 [164 kB] Get: 103 http://deb.debian.org/debian trixie/main amd64 libhwloc-dev amd64 2.10.0-1+b1 [250 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b1 [51.9 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.9-1+b1 [18.1 kB] Get: 106 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b1 [24.3 kB] Get: 107 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2 [144 kB] Get: 108 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get: 109 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.7-1+b1 [799 kB] Get: 110 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get: 111 http://deb.debian.org/debian trixie/main amd64 libxnvctrl0 amd64 535.171.04-1 [13.8 kB] Get: 112 http://deb.debian.org/debian trixie/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b1 [40.3 kB] Get: 113 http://deb.debian.org/debian trixie/main amd64 libhwloc-plugins amd64 2.10.0-1+b1 [18.0 kB] Get: 114 http://deb.debian.org/debian trixie/main amd64 libnl-3-dev amd64 3.7.0-0.3 [99.4 kB] Get: 115 http://deb.debian.org/debian trixie/main amd64 libnl-route-3-dev amd64 3.7.0-0.3 [199 kB] Get: 116 http://deb.debian.org/debian trixie/main amd64 libibverbs-dev amd64 50.0-2+b1 [642 kB] Get: 117 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 118 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 119 http://deb.debian.org/debian trixie/main amd64 libmunge2 amd64 0.5.15-4 [19.8 kB] Get: 120 http://deb.debian.org/debian trixie/main amd64 libpmix2t64 amd64 5.0.2-3 [652 kB] Get: 121 http://deb.debian.org/debian trixie/main amd64 libucx0 amd64 1.16.0+ds-5 [1109 kB] Get: 122 http://deb.debian.org/debian trixie/main amd64 libopenmpi3t64 amd64 4.1.6-13.3 [2426 kB] Get: 123 http://deb.debian.org/debian trixie/main amd64 openmpi-common all 4.1.6-13.3 [169 kB] Get: 124 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] Get: 125 http://deb.debian.org/debian trixie/main amd64 libpmix-dev amd64 5.0.2-3 [3940 kB] Get: 126 http://deb.debian.org/debian trixie/main amd64 openmpi-bin amd64 4.1.6-13.3 [226 kB] Get: 127 http://deb.debian.org/debian trixie/main amd64 libopenmpi-dev amd64 4.1.6-13.3 [972 kB] Get: 128 http://deb.debian.org/debian trixie/main amd64 libsprng2 amd64 2.0a-13 [75.8 kB] Get: 129 http://deb.debian.org/debian trixie/main amd64 libsprng2-dev amd64 2.0a-13 [77.9 kB] Get: 130 http://deb.debian.org/debian trixie/main amd64 mpi-default-dev amd64 1.15 [3152 B] Get: 131 http://deb.debian.org/debian trixie/main amd64 time amd64 1.9-0.2 [50.8 kB] Fetched 133 MB in 8s (16.6 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19701 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-7_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../001-libproc2-0_2%3a4.0.4-4_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-4) ... Selecting previously unselected package procps. 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.3) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libssh2-1t64:amd64 (1.11.0-5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libfido2-1:amd64 (1.14.0-1+b2) ... Setting up libgfortran-13-dev:amd64 (13.2.0-25) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b3) ... Setting up liblocale-gettext-perl (1.07-7) ... Setting up chrpath (0.16-2+b1) ... Setting up libsprng2 (2.0a-13) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b1) ... Setting up libxcb1:amd64 (1.17.0-2) ... Setting up gettext (0.21-14+b1) ... 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Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3) ... Setting up groff-base (1.23.0-4) ... Setting up libsprng2-dev (2.0a-13) ... Setting up libx11-6:amd64 (2:1.8.7-1+b1) ... Setting up libhwloc-dev:amd64 (2.10.0-1+b1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b1) ... Setting up libarchive13t64:amd64 (3.7.2-2.1) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up libibverbs1:amd64 (50.0-2+b1) ... Setting up libcurl4t64:amd64 (8.8.0-1) ... Setting up ibverbs-providers:amd64 (50.0-2+b1) ... Setting up openssh-client (1:9.7p1-5) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxnvctrl0:amd64 (535.171.04-1) ... Setting up libnl-route-3-dev:amd64 (3.7.0-0.3) ... Setting up libevent-dev (2.1.12-stable-10) ... Setting up cmake (3.29.4-1) ... Setting up librdmacm1t64:amd64 (50.0-2+b1) ... Setting up libhsakmt1:amd64 (5.7.0-1) ... Setting up libfabric1:amd64 (1.17.0-3+b1) ... Setting up debhelper (13.15.3) ... Setting up libibverbs-dev:amd64 (50.0-2+b1) ... Setting up libhwloc-plugins:amd64 (2.10.0-1+b1) ... Setting up libpmix2t64:amd64 (5.0.2-3) ... Setting up libhsa-runtime64-1 (5.7.1-2) ... Setting up libpmix-dev:amd64 (5.0.2-3) ... Setting up libamdhip64-5 (5.7.1-3) ... Setting up libucx0:amd64 (1.16.0+ds-5) ... Setting up libopenmpi3t64:amd64 (4.1.6-13.3) ... Setting up openmpi-bin (4.1.6-13.3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.6-13.3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.15) ... Processing triggers for libc-bin (2.38-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../iqtree_2.0.7+dfsg-1_source.changes dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/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 cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- clang-tidy not found. -- Configuring done (16.2s) -- Generating done (1.1s) 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 cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- clang-tidy not found. -- Configuring done (13.5s) -- Generating done (0.6s) 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 cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 13.2.0 -- The CXX compiler identification is GNU 13.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.83.0/BoostConfig.cmake (found version "1.83.0") IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") Using system zlib CMake Deprecation Warning at yaml-cpp/CMakeLists.txt:5 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success CMake Deprecation Warning at terraphast/CMakeLists.txt:3 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- clang-tidy not found. -- Configuring done (42.4s) -- Generating done (0.5s) 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 -j20 "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[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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 /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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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 /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/kernelavx.dir/DependInfo.cmake "--color=" 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/kernelfma.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]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.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/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[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 -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' 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' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.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/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[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' 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 -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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/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 -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' 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/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' 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/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.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/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o [ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o [ 5%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 6%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 2%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o [ 7%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.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)); | ^~~~~~~~~~~~~~~~~~ [ 8%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 8%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c [ 8%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c [ 8%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/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.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c [ 8%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 9%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c [ 9%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.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); | ^~~~~~~~~~~~~~~~~~ /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 C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 11%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c 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); | ^~~~~~~~~~~~~~~ [ 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c [ 12%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 12%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 13%] 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' [ 13%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.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/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[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 14%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 14%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 14%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxscharactersblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 15%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/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/ncl/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 15%] 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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 /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.omp' [ 15%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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/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=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build /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)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' In file included from /usr/include/c++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ [ 16%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 17%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 17%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 17%] 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 [ 18%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp 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 [ 18%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 18%] Built target gsl 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.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/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=" [ 18%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 19%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c [ 20%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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); | ^~~~~~~~~~~~~~~~~~ [ 20%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/ncl/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 20%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ [ 20%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/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); | ^~~~~~~~~~~~~~~~~~~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/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/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 21%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 22%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 23%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c [ 24%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.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); | ~~~~~~^~~~~~~~ [ 24%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c [ 25%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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)); | ^~~~~~~~~~~~~~~~~~ [ 25%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.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); | ^~~~~~~~~~~~~~~ [ 25%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/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/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/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 26%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 26%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c [ 27%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 28%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.c [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/nxsstring.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 29%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 30%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 30%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 31%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 31%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c [ 31%] 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 /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' [ 32%] 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 [ 32%] Built target lbfgsb make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.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/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/pllavx.dir/DependInfo.cmake "--color=" 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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' /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 [ 32%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 32%] Built target booster make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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=" 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' [ 32%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/ncl/nxstreesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 33%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 33%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 34%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 34%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c [ 34%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 34%] 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/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); | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /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/newviewGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 36%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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': [ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o /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); | ^~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /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)); | ^~~~~~~~~~~~~~~~~~ [ 36%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 36%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 36%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c [ 37%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o [ 39%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 39%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 39%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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); | ^~~~~~~~~~~~~~~ [ 40%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 40%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 41%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/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); | ^~~~~~~~~~~~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 41%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c [ 42%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/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); | ^~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ [ 42%] 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 [ 42%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o [ 42%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c /usr/bin/ranlib libncl.a 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); | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 42%] Built target ncl 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=" 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' [ 42%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c [ 43%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.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); | ^~~~~~~~~~~~~~~ [ 44%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c [ 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 44%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c [ 44%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 45%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.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/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' 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%] Built target pllavx 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=" 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) * | ^~~~~~~~~~~~~~~~~~ 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' [ 45%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 45%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/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/utils/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 46%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 47%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 47%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 47%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 48%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 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.omp/yaml-cpp && /usr/bin/c++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 50%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.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)" | ^~~~~~~ [ 51%] 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 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 [ 51%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 51%] Built target whtest [ 51%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/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/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] 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' [ 52%] 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 [ 52%] Linking CXX static library libterraphast.a 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/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake 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 [ 52%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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' [ 52%] Built target terraphast [ 53%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/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/tools.cpp:25: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 54%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 54%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 55%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 55%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp [ 55%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 56%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.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/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 58%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 59%] 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 /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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 59%] Built target pll [ 60%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 61%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 61%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 62%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 62%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 63%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 64%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 64%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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) { | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 66%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 67%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 68%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/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/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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 /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' [ 69%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/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' [ 69%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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 /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' [ 69%] 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=" 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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 69%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp [ 69%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 70%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 70%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 70%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp [ 71%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 71%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o [ 72%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 73%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp [ 74%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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) { | ^~~~~ 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); | ^~~~~ [ 74%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.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/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*) { | ^~~~~ /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/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*); | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o 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); | ^~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp /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*); | ^~~~~ [ 75%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 75%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 76%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 76%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.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/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 77%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp [ 78%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 78%] 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 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 /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 [ 78%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 78%] 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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.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*); | ^~~~~ [ 80%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 80%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/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); | ^~~~~ /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) { | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/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*); | ^~~~~ [ 81%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp [ 82%] Linking CXX static library libphyloYAML.a In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake [ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o 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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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' [ 82%] Built target phyloYAML /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 | ^~~~~~~~ [ 83%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.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*); | ^~~~~ [ 83%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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); | ^~~~~ /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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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); | ^~~~~ 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*); | ^~~~~ /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 | } | ^ [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp' [ 84%] Built target kernelsse [ 85%] 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' [ 85%] Built target main [ 85%] 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 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-I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 88%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 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-Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o [ 93%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/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.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/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.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.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/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*); | ^~~~~ [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.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); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o /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*); | ^~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 | } | ^ [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] 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' [ 99%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/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 cd build.serial && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 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 make -f CMakeFiles/Makefile2 all 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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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 -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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/kernelavx.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.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/kernelfma.dir/DependInfo.cmake "--color=" make[4]: Entering directory 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"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' 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/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]: Leaving 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' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build 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[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' 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.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' 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 && /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=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build 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[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o 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=" /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' 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/build 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]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build 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=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' 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.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp [ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.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/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build [ 2%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp [ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 2%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o [ 3%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c [ 4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c 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/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 6%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 7%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o [ 7%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.c [ 8%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 9%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.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); | ^~~~~~~~~~~~~~~ [ 9%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o 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); | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c 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)); | ^~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ [ 9%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c [ 9%] 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 [ 9%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp 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 [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c /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.serial' [ 10%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 11%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 11%] Built target vectorclass make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 11%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o 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/pllavx.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 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 [ 12%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 13%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp 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 [ 13%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp /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' 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); | ^~~~~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~~~~ [ 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.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 terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 13%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c [ 13%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 14%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c [ 15%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 15%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c [ 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c [ 17%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /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 terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 17%] 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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ 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 /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' [ 17%] Built target gsl [ 18%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/nxsassumptionsblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 18%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 18%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashtables_bfields.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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c [ 18%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /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.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 19%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c [ 19%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 20%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 21%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 21%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c [ 22%] 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 -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.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)); | ^~~~~~~~~~~~~~~~~~ [ 23%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 23%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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); | ^~~~~~~~~~~~~~~ [ 23%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 23%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 23%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 23%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 24%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 24%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 25%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 26%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c [ 26%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 26%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.c [ 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 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); | ^~~~~~~~~~~~~~~~~~ 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 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function 'newviewAncestralIterative': /usr/bin/ranlib libbooster.a /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' [ 27%] Built target booster [ 28%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 29%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 29%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 29%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 29%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/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/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/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/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/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/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 30%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] 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 [ 31%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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 /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' [ 31%] 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=" 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' [ 31%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 32%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.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/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 33%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 33%] Built target pllavx [ 33%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c [ 34%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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); | ^~~~~~~~~~~~~~~ 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/ncl/nxsdatablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 34%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ [ 35%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 35%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 35%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 35%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 36%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 37%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 38%] 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 /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 [ 38%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 38%] Built target whtest [ 38%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 38%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 38%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 38%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 39%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.c 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); | ^~~~~~~~~~~~~~~ [ 39%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c [ 40%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c [ 41%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 41%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/topologies.c [ 42%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c [ 42%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/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/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); | ^~~~~~~~~~~~~~~ [ 42%] 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 -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/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/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 43%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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) * | ^~~~~~~~~~~~~~~~~~ [ 43%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 45%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 45%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 47%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 47%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.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/utils/pllnni.cpp:34: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 48%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 48%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 48%] 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 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 [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o /usr/bin/ranlib libterraphast.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 49%] Built target terraphast [ 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public 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/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] 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 /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' [ 50%] Built target pll [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 51%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 52%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 52%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 53%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 53%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 53%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 54%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 54%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 55%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 55%] 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++ -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 55%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 56%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 57%] 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 [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 57%] 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' [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 59%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 59%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 60%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o [ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o [ 61%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 61%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 62%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 63%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 63%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp [ 64%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 65%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] 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' [ 66%] 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' [ 66%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp [ 66%] 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 /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' [ 66%] 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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 66%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o [ 67%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 67%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o [ 67%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 68%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp [ 69%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.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)" | ^~~~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/alignmentpairwise.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/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/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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 /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' [ 69%] 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' /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) { | ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o [ 70%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o [ 71%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 72%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o [ 72%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 73%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o [ 74%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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); | ^~~~~ /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/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/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/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*); | ^~~~~ [ 74%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 75%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 75%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 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 /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 [ 76%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/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/ratemeyerhaeseler.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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.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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/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/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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/model/ratekategory.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 78%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/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/ratefree.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 78%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 78%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/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/main.cpp:37: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] 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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /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' [ 80%] Built target phyloYAML [ 80%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 81%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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*); | ^~~~~ [ 81%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.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*); | ^~~~~ /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) { | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/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/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ 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*); | ^~~~~ /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: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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp [ 83%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 83%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.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 | ^~~~~~~~ [ 83%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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); | ^~~~~ 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*); | ^~~~~ /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/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: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/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 | } | ^ [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' [ 84%] Built target kernelsse [ 85%] 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[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/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.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST 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-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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 90%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/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/phylotreepars.cpp:10: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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/supernode.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.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/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/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*); | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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*); | ^~~~~ [ 97%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 | } | ^ [ 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] 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' [ 99%] 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++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/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' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1 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 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[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/kernelsse.dir/DependInfo.cmake "--color=" make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.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/kernelavx.dir/DependInfo.cmake "--color=" make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/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/kernelfma.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' 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/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=" make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build 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/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' 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/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=" make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build 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/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/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.mpi' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o 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/depend 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/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color=" /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend 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=" make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color=" 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/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' 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 && /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.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o [ 2%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' 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/terraphast && /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 2%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 3%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/alignment.c [ 3%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o [ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/lcg64.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 6%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 8%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 9%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/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); | ^~~~~~~~~~~~~~~ [ 9%] 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 /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' [ 9%] 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' [ 9%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/hashmap.c [ 9%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen.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)); | ^~~~~~~~~~~~~~~~~~ [ 9%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 10%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 10%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/io.c [ 10%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/memory.c [ 11%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/sort.c [ 12%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/store.c [ 12%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree.c [ 12%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 13%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 13%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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/primes-lcg64.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/primes-lcg64.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); | ^~~~~~~~~~~~~~~~~~ /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); | ^~~~~~~~~~~~~~~~~~ [ 14%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 14%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/sprng/checkid.c [ 14%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 15%] 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' [ 15%] Built target sprng make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.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/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 15%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 15%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gaussinv.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 16%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 16%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 16%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 17%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 18%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /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); | ^~~~~~~~~~~~~~~ [ 18%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 18%] 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/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); | ^~~~~~~~~~~~~~~ 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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libgsl.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 18%] Built target gsl 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' [ 18%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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); | ^~~~~~~~~~~~~~~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/nxsdiscretematrix.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 19%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c /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++/13/bits/stl_function.h:1438: /usr/include/c++/13/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ /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); | ~~~~~~^~~~~~~~ [ 20%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 21%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 22%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 22%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/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/nxsdiscretedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 22%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/prng.c [ 22%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c [ 23%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/stats.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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 23%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 24%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 25%] Building C object pll/CMakeFiles/pll.dir/hash.c.o [ 25%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/hash.c cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/random.c [ 25%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 In 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/phylotreeavx.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 26%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 26%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/lexer.c [ 27%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 27%] 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 [ 28%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda.c 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 [ 28%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.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/tree/phylokernel.h:11, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp:11: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 28%] 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=" [ 28%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c [ 28%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/booster/tree_utils.c 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' 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); | ^~~~~~~~~~~~~~~ [ 28%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp 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)); | ^~~~~~~~~~~~~~~~~~ [ 29%] 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 /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)); | ^~~~~~~~~~~~~~~~~~ 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 [ 29%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 29%] Built target booster [ 29%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 29%] 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/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); | ^~~~~~~~~~~~~~~ cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 29%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest.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/nxsdistancedatum.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 30%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/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/nxsdistancesblock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/eigendecomposition.cpp:26: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /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 ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 31%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 31%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/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/nxsexception.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 31%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 31%] Building C object pll/CMakeFiles/pll.dir/newick.c.o [ 32%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c [ 32%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.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); | ^~~~~~~~~~~~~~~ [ 33%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 34%] Linking C static library libpllavx.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 [ 35%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 35%] Built target pllavx [ 35%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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)); | ^~~~~~~~~~~~~~~~~~ [ 36%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/nxsreader.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 37%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 37%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 37%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 37%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 38%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 39%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 39%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 39%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 40%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.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/nxstaxablock.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/genericParallelization.c [ 40%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o [ 41%] Linking CXX static library libwhtest.a cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 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' [ 41%] Built target whtest [ 42%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 43%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 43%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/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/ncl/nxstoken.cpp:19: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 43%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 43%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/queue.c [ 44%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.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); | ^~~~~~~~~~~~~~~ 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); | ^~~~~~~~~~~~~~~ [ 44%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/recom.c [ 45%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/restartHashTable.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); | ^~~~~~~~~~~~~~~ [ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 45%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/ssort.c 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); | ^~~~~~~~~~~~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 46%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/stack.c [ 46%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/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/utils/optimization.cpp:18: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 47%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/trash.c [ 47%] 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 -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/treeIO.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); | ^~~~~~~~~~~~~~~ [ 47%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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/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); | ^~~~~~~~~~~~~~~ [ 47%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pll/utils.c [ 48%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp [ 48%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 48%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.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) * | ^~~~~~~~~~~~~~~~~~ [ 49%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/map:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 50%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 50%] 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 [ 51%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a In file included from /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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' [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o [ 51%] Built target terraphast cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 51%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 52%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 52%] 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 [ 53%] 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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 53%] 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.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=" /usr/bin/ranlib libnclextra.a 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' [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o [ 54%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 54%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 54%] 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' [ 54%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 54%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 54%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 55%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 55%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 56%] 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 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' [ 56%] Built target pll [ 57%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 57%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 57%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 58%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 58%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 58%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 /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)" | ^~~~~~~ [ 60%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 60%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -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 [ 60%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 61%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 61%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 62%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 62%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 62%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 62%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 64%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24: /usr/include/c++/13/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/alignment/alignment.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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.mpi/pda && /usr/bin/cc -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/lpwrapper.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 65%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 65%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/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.mpi/pda && /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 66%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp [ 67%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 68%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/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/pda/pdtree.cpp:20: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/fstream:40, from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/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++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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 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' [ 69%] Built target yaml-cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/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' [ 69%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp /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) { | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 69%] 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' [ 69%] 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' [ 70%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o [ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o [ 71%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 72%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 72%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 73%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp [ 74%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 74%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public 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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/rategamma.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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*); | ^~~~~ /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); | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp 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*); | ^~~~~ /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*) { | ^~~~~ /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/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/ratemeyerhaeseler.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/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/model/ratemeyerdiscrete.cpp:21: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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) { | ^~~~~ [ 75%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 76%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 76%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake [ 77%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp 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 In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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' [ 77%] 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=" 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' [ 78%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp [ 78%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp [ 78%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 | ^~~~~~~~ [ 78%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp [ 79%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.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/rateheterotachy.cpp:9: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 80%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 80%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.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*) { | ^~~~~ In 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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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*); | ^~~~~ [ 80%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.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/modelmixture.cpp:8: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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) { | ^~~~~ 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/modelpomomixture.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp [ 82%] 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' [ 82%] Built target phyloYAML [ 82%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/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/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/string:49, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/istream:40, from /usr/include/c++/13/sstream:40, from /usr/include/c++/13/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++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 83%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 83%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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/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/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 | } | ^ [ 84%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi' [ 84%] Built target kernelsse [ 85%] 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 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-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 [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o [ 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o [ 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/phylotree.cpp:22: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/quartet.cpp:12: /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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/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*); | ^~~~~ 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/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*); | ^~~~~ [ 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/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.mpi/tree && /usr/bin/c++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_tree.h:65, from /usr/include/c++/13/set:62, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25: /usr/include/c++/13/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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ [ 99%] 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' [ 99%] 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++ -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/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 172 | : public binary_function | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25: /usr/include/c++/13/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 -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/reproducible-path/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/reproducible-path/iqtree-2.0.7+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a make[4]: Leaving directory '/build/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 ... + /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: i-capture-the-hostname (AVX, 78 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy Seed: 502790 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Jun 7 19:48:12 2024 Kernel: AVX - 1 threads (20 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 20 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.019 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: -11231.490 Optimal log-likelihood: -11231.050 Rate parameters: A-C: 1.37829 A-G: 2.22792 A-T: 1.67169 C-G: 1.83854 C-T: 2.67788 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.521 Parameters optimization took 1 rounds (0.286 sec) Time for fast ML tree search: 1.666 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11793.947 93 23773.895 23834.184 24141.304 2 GTR+F+I 11551.789 94 23291.578 23353.377 23662.938 3 GTR+F+G4 11247.563 94 22683.127 22744.926 23054.487 4 GTR+F+I+G4 11231.063 95 22652.126 22715.459 23027.437 5 GTR+F+R2 11344.614 95 22879.228 22942.562 23254.539 6 GTR+F+R3 11232.918 97 22659.836 22726.312 23043.049 7 GTR+F+R4 11226.328 99 22650.656 22720.374 23041.769 8 GTR+F+R5 11225.945 101 22653.890 22726.954 23052.905 17 SYM+I+G4 11234.267 92 22652.533 22711.338 23015.993 30 TVM+F+I+G4 11233.693 94 22655.386 22717.186 23026.747 43 TVMe+I+G4 11236.278 91 22654.555 22711.898 23014.064 56 TIM3+F+I+G4 11244.326 93 22674.652 22734.942 23042.062 69 TIM3e+I+G4 11248.181 90 22676.363 22732.267 23031.921 82 TIM2+F+I+G4 11247.451 93 22680.902 22741.192 23048.312 95 TIM2e+I+G4 11254.880 90 22689.760 22745.664 23045.318 108 TIM+F+I+G4 11235.336 93 22656.672 22716.962 23024.082 121 TIMe+I+G4 11241.998 90 22663.996 22719.900 23019.554 134 TPM3u+F+I+G4 11246.998 92 22677.996 22736.800 23041.455 147 TPM3+F+I+G4 11246.998 92 22677.996 22736.800 23041.455 160 TPM2u+F+I+G4 11250.043 92 22684.086 22742.891 23047.546 173 TPM2+F+I+G4 11250.043 92 22684.086 22742.891 23047.546 186 K3Pu+F+I+G4 11237.916 92 22659.832 22718.636 23023.291 199 K3P+I+G4 11243.848 89 22665.697 22720.187 23017.304 212 TN+F+I+G4 11247.474 92 22678.947 22737.751 23042.406 225 TNe+I+G4 11254.878 89 22687.756 22742.246 23039.363 238 HKY+F+I+G4 11250.077 91 22682.154 22739.496 23041.662 251 K2P+I+G4 11256.741 88 22689.481 22742.580 23037.138 264 F81+F+I+G4 11297.086 90 22774.173 22830.077 23129.730 277 JC+I+G4 11301.119 87 22776.237 22827.967 23119.943 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 8.756 seconds (0h:0m:8s) Wall-clock time for ModelFinder: 25.743 seconds (0h:0m:25s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.566 / Estimate: 0.000, 0.965 / LogL: -11251.735 Init pinv, alpha: 0.012, 1.566 / Estimate: 0.084, 1.554 / LogL: -11236.279 Init pinv, alpha: 0.023, 1.566 / Estimate: 0.084, 1.558 / LogL: -11236.275 Init pinv, alpha: 0.035, 1.566 / Estimate: 0.084, 1.556 / LogL: -11236.277 Init pinv, alpha: 0.046, 1.566 / Estimate: 0.084, 1.559 / LogL: -11236.277 Init pinv, alpha: 0.058, 1.566 / Estimate: 0.084, 1.556 / LogL: -11236.281 Init pinv, alpha: 0.069, 1.566 / Estimate: 0.083, 1.553 / LogL: -11236.283 Init pinv, alpha: 0.081, 1.566 / Estimate: 0.084, 1.557 / LogL: -11236.279 Init pinv, alpha: 0.093, 1.566 / Estimate: 0.085, 1.568 / LogL: -11236.277 Init pinv, alpha: 0.104, 1.566 / Estimate: 0.085, 1.574 / LogL: -11236.284 Optimal pinv,alpha: 0.084, 1.558 / LogL: -11236.275 Parameters optimization took 11.832 sec Computing ML distances based on estimated model parameters... 0.069 sec Computing BIONJ tree... 0.003 seconds Log-likelihood of BIONJ tree: -11270.870 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 4.067 second Computing log-likelihood of 98 initial trees ... 9.126 seconds Current best score: -11236.275 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11231.529 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 4: -11226.728 Iteration 10 / LogL: -11244.648 / Time: 0h:0m:35s Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 13: -11226.439 Iteration 20 / LogL: -11228.102 / Time: 0h:0m:46s Finish initializing candidate tree set (14) Current best tree score: -11226.439 / CPU time: 34.040 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 23: -11225.475 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 24: -11224.871 Iteration 30 / LogL: -11224.901 / Time: 0h:1m:2s (0h:3m:23s left) Iteration 40 / LogL: -11225.483 / Time: 0h:1m:15s (0h:2m:43s left) Iteration 50 / LogL: -11249.423 / Time: 0h:1m:29s (0h:2m:14s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 55: -11224.158 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 57: -11224.115 BETTER TREE FOUND at iteration 60: -11224.108 Iteration 60 / LogL: -11224.108 / Time: 0h:1m:43s (0h:2m:55s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 63: -11222.776 Iteration 70 / LogL: -11224.173 / Time: 0h:2m:0s (0h:2m:42s left) Iteration 80 / LogL: -11223.090 / Time: 0h:2m:13s (0h:2m:20s left) Iteration 90 / LogL: -11222.781 / Time: 0h:2m:29s (0h:2m:2s left) Iteration 100 / LogL: -11222.826 / Time: 0h:2m:44s (0h:1m:44s left) Iteration 110 / LogL: -11226.536 / Time: 0h:2m:56s (0h:1m:25s left) UPDATE BEST LOG-LIKELIHOOD: -11222.775 Iteration 120 / LogL: -11223.885 / Time: 0h:3m:5s (0h:1m:7s left) Iteration 130 / LogL: -11222.941 / Time: 0h:3m:16s (0h:0m:50s left) Iteration 140 / LogL: -11222.828 / Time: 0h:3m:25s (0h:0m:34s left) UPDATE BEST LOG-LIKELIHOOD: -11222.775 Iteration 150 / LogL: -11231.548 / Time: 0h:3m:33s (0h:0m:18s left) Iteration 160 / LogL: -11227.663 / Time: 0h:3m:43s (0h:0m:4s left) TREE SEARCH COMPLETED AFTER 164 ITERATIONS / Time: 0h:3m:48s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.775 Optimal log-likelihood: -11222.773 Rate parameters: A-C: 1.51152 A-G: 2.60282 A-T: 1.66838 C-G: 1.97565 C-T: 2.60282 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.530 Parameters optimization took 1 rounds (0.259 sec) BEST SCORE FOUND : -11222.773 Total tree length: 12.599 Total number of iterations: 164 CPU time used for tree search: 68.581 sec (0h:1m:8s) Wall-clock time used for tree search: 215.616 sec (0h:3m:35s) Total CPU time used: 72.531 sec (0h:1m:12s) Total wall-clock time used: 228.392 sec (0h:3m:48s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Fri Jun 7 19:52:26 2024 real 4m14.208s user 1m21.303s sys 0m1.190s + /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 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: i-capture-the-hostname (AVX, 78 GB RAM) Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo Seed: 726303 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Jun 7 19:52:26 2024 Kernel: AVX - 1 threads (20 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 20 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 44 sequences with 384 columns, 355 distinct patterns 322 parsimony-informative, 22 singleton sites, 40 constant sites Gap/Ambiguity Composition p-value 1 FL-1-103 19.53% failed 0.00% 2 OSH-1-103 19.53% failed 0.00% 3 CEU-1-103 19.53% failed 0.79% 4 TH-1-103 19.53% failed 0.10% 5 CAa1-103 19.53% failed 0.14% 6 CAb1-103 19.53% failed 0.00% 7 SI-1-103 19.53% failed 0.00% 8 LU-1-103 19.53% failed 0.01% 9 SU-1-103 19.53% failed 0.00% 10 RP-56-175 6.25% failed 4.72% 11 A-14-133 6.25% failed 3.08% 12 PR-57-176 6.25% passed 63.84% 13 PY-61-180 6.25% passed 69.25% 14 MGI-58-176 7.03% failed 0.05% 15 SCR-58-177 6.25% passed 94.64% 16 SA-60-179 6.25% passed 66.43% 17 BR-60-179 6.25% passed 27.40% 18 CPL-58-177 6.25% passed 55.10% 19 LTU-59-178 6.25% passed 28.43% 20 TSP-58-177 6.25% passed 51.74% 21 YBN-56-175 6.25% passed 72.08% 22 AN-56-175 6.25% passed 52.14% 23 HI-60-179 6.25% passed 51.36% 24 ANA-56-175 6.25% passed 88.34% 25 ZE-48-166 7.03% failed 0.05% 26 EAT-48-166 7.03% passed 14.40% 27 YSA-46-164 7.03% passed 6.42% 28 TH-52-170 7.03% passed 20.58% 29 LA-68-186 7.03% passed 10.46% 30 GR-854-978 2.34% failed 0.02% 31 MO-29-154 1.56% failed 0.00% 32 OE-36-161 1.56% passed 15.04% 33 EME-43-168 1.56% failed 1.16% 34 LRE-46-171 1.56% failed 0.00% 35 P6-2-107 17.19% passed 44.21% 36 HO-1-106 17.19% passed 14.57% 37 SP-1-106 17.19% failed 2.41% 38 PA-1-105 17.97% failed 0.00% 39 NE-2-109 15.62% passed 53.11% 40 IFE-2-109 15.62% passed 63.82% 41 HS-9-115 16.41% failed 0.03% 42 RVI-7-114 15.62% failed 0.12% 43 IFE-8-115 15.62% passed 39.01% 44 RVI-5-112 15.62% failed 0.04% **** TOTAL 10.87% 22 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.009 seconds Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -11226.808 Optimal log-likelihood: -11226.430 Rate parameters: A-C: 1.45392 A-G: 2.33679 A-T: 1.75868 C-G: 1.91140 C-T: 2.80714 G-T: 1.00000 Base frequencies: A: 0.249 C: 0.262 G: 0.251 T: 0.239 Proportion of invariable sites: 0.085 Gamma shape alpha: 1.528 Parameters optimization took 1 rounds (0.208 sec) Time for fast ML tree search: 1.803 seconds NOTE: ModelFinder requires 5 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 384) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 11788.646 93 23763.291 23823.581 24130.701 2 GTR+F+I 11546.831 94 23281.661 23343.461 23653.022 3 GTR+F+G4 11242.397 94 22672.793 22734.593 23044.154 4 GTR+F+I+G4 11226.436 95 22642.871 22706.205 23018.182 5 GTR+F+R2 11335.984 95 22861.969 22925.302 23237.280 6 GTR+F+R3 11227.934 97 22649.868 22716.344 23033.081 7 GTR+F+R4 11220.419 99 22638.837 22708.555 23029.951 8 GTR+F+R5 11220.138 101 22642.276 22715.340 23041.291 17 SYM+I+G4 11229.371 92 22642.742 22701.546 23006.201 30 TVM+F+I+G4 11228.989 94 22645.979 22707.778 23017.339 43 TVMe+I+G4 11231.294 91 22644.587 22701.930 23004.096 56 TIM3+F+I+G4 11240.764 93 22667.528 22727.818 23034.938 69 TIM3e+I+G4 11244.383 90 22668.765 22724.670 23024.323 82 TIM2+F+I+G4 11244.301 93 22674.601 22734.891 23042.011 95 TIM2e+I+G4 11251.824 90 22683.648 22739.553 23039.206 108 TIM+F+I+G4 11231.812 93 22649.623 22709.913 23017.033 121 TIMe+I+G4 11238.408 90 22656.816 22712.721 23012.374 134 TPM3u+F+I+G4 11243.465 92 22670.930 22729.734 23034.389 147 TPM3+F+I+G4 11243.465 92 22670.930 22729.734 23034.389 160 TPM2u+F+I+G4 11246.900 92 22677.800 22736.604 23041.259 173 TPM2+F+I+G4 11246.900 92 22677.800 22736.604 23041.259 186 K3Pu+F+I+G4 11234.314 92 22652.629 22711.433 23016.088 199 K3P+I+G4 11240.168 89 22658.335 22712.825 23009.942 212 TN+F+I+G4 11244.447 92 22672.894 22731.698 23036.353 225 TNe+I+G4 11251.881 89 22681.762 22736.252 23033.369 238 HKY+F+I+G4 11247.069 91 22676.138 22733.481 23035.647 251 K2P+I+G4 11253.728 88 22683.456 22736.554 23031.112 264 F81+F+I+G4 11295.793 90 22771.586 22827.490 23127.143 277 JC+I+G4 11299.726 87 22773.452 22825.182 23117.158 Akaike Information Criterion: GTR+F+R4 Corrected Akaike Information Criterion: SYM+I+G4 Bayesian Information Criterion: TVMe+I+G4 Best-fit model: TVMe+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 9.071 seconds (0h:0m:9s) Wall-clock time for ModelFinder: 21.271 seconds (0h:0m:21s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.574 / Estimate: 0.000, 0.963 / LogL: -11246.220 Init pinv, alpha: 0.012, 1.574 / Estimate: 0.084, 1.567 / LogL: -11231.287 Init pinv, alpha: 0.023, 1.574 / Estimate: 0.084, 1.564 / LogL: -11231.290 Init pinv, alpha: 0.035, 1.574 / Estimate: 0.084, 1.563 / LogL: -11231.292 Init pinv, alpha: 0.046, 1.574 / Estimate: 0.084, 1.566 / LogL: -11231.290 Init pinv, alpha: 0.058, 1.574 / Estimate: 0.084, 1.563 / LogL: -11231.296 Init pinv, alpha: 0.069, 1.574 / Estimate: 0.083, 1.560 / LogL: -11231.299 Init pinv, alpha: 0.081, 1.574 / Estimate: 0.084, 1.564 / LogL: -11231.294 Init pinv, alpha: 0.093, 1.574 / Estimate: 0.085, 1.576 / LogL: -11231.291 Init pinv, alpha: 0.104, 1.574 / Estimate: 0.085, 1.582 / LogL: -11231.299 Optimal pinv,alpha: 0.084, 1.567 / LogL: -11231.287 Parameters optimization took 13.999 sec Computing ML distances based on estimated model parameters... 0.065 sec Computing BIONJ tree... 0.007 seconds Log-likelihood of BIONJ tree: -11270.762 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 3.059 second Computing log-likelihood of 98 initial trees ... 8.262 seconds Current best score: -11231.287 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -11231.265 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 3: -11225.129 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 4: -11224.928 Iteration 10 / LogL: -11231.838 / Time: 0h:0m:39s Iteration 20 / LogL: -11226.793 / Time: 0h:0m:50s Finish initializing candidate tree set (13) Current best tree score: -11224.928 / CPU time: 35.843 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -11228.537 / Time: 0h:1m:0s (0h:2m:35s left) Iteration 40 / LogL: -11229.017 / Time: 0h:1m:5s (0h:1m:48s left) Iteration 50 / LogL: -11225.053 / Time: 0h:1m:15s (0h:1m:23s left) Iteration 60 / LogL: -11228.563 / Time: 0h:1m:25s (0h:1m:4s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 70: -11224.082 Iteration 70 / LogL: -11224.082 / Time: 0h:1m:41s (0h:2m:26s left) Iteration 80 / LogL: -11229.154 / Time: 0h:1m:54s (0h:2m:10s left) Iteration 90 / LogL: -11291.951 / Time: 0h:2m:6s (0h:1m:54s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 98: -11223.409 Iteration 100 / LogL: -11225.298 / Time: 0h:2m:22s (0h:2m:20s left) Iteration 110 / LogL: -11224.619 / Time: 0h:2m:37s (0h:2m:7s left) Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 118: -11222.772 Iteration 120 / LogL: -11224.465 / Time: 0h:2m:52s (0h:2m:22s left) Iteration 130 / LogL: -11232.834 / Time: 0h:3m:6s (0h:2m:6s left) Iteration 140 / LogL: -11223.689 / Time: 0h:3m:17s (0h:1m:50s left) Iteration 150 / LogL: -11225.844 / Time: 0h:3m:31s (0h:1m:36s left) Iteration 160 / LogL: -11224.331 / Time: 0h:3m:44s (0h:1m:22s left) Iteration 170 / LogL: -11222.919 / Time: 0h:4m:2s (0h:1m:8s left) Iteration 180 / LogL: -11222.790 / Time: 0h:4m:18s (0h:0m:54s left) Iteration 190 / LogL: -11224.442 / Time: 0h:4m:32s (0h:0m:40s left) Iteration 200 / LogL: -11223.203 / Time: 0h:4m:45s (0h:0m:25s left) Iteration 210 / LogL: -11222.974 / Time: 0h:5m:3s (0h:0m:11s left) TREE SEARCH COMPLETED AFTER 219 ITERATIONS / Time: 0h:5m:19s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -11222.772 Optimal log-likelihood: -11222.772 Rate parameters: A-C: 1.51770 A-G: 2.61286 A-T: 1.67516 C-G: 1.98341 C-T: 2.61286 G-T: 1.00000 Base frequencies: A: 0.250 C: 0.250 G: 0.250 T: 0.250 Proportion of invariable sites: 0.084 Gamma shape alpha: 1.530 Parameters optimization took 1 rounds (0.448 sec) BEST SCORE FOUND : -11222.772 Total tree length: 12.602 Total number of iterations: 219 CPU time used for tree search: 90.959 sec (0h:1m:30s) Wall-clock time used for tree search: 304.823 sec (0h:5m:4s) Total CPU time used: 95.068 sec (0h:1m:35s) Total wall-clock time used: 319.669 sec (0h:5m:19s) 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: Fri Jun 7 19:58:07 2024 real 5m41.040s user 1m44.158s sys 0m1.554s + rm -rf /tmp/iqtree-test.cw8mH0 185.50user 2.84system 9:55.90elapsed 31%CPU (0avgtext+0avgdata 14824maxresident)k 2240inputs+1208outputs (2major+8835minor)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 -j20 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 -j20 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' in '../iqtree_2.0.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2616740/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/2616740 and its subdirectories I: Current time: Sat Jun 8 10:08:03 +14 2024 I: pbuilder-time-stamp: 1717790883