Diff of the two buildlogs:

--
--- b1/build.log	2024-11-05 18:18:07.762063604 +0000
+++ b2/build.log	2024-11-05 17:31:44.661042427 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Tue Nov  5 05:31:47 -12 2024
-I: pbuilder-time-stamp: 1730827907
+I: Current time: Tue Dec  9 13:47:14 +14 2025
+I: pbuilder-time-stamp: 1765237634
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -26,52 +26,84 @@
 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/306718/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1465381/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos5-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 Dec  8 23:47 /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/1465381/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1465381/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  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]="32" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.32(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=42 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='fdb74007746d41289eac2be145ab1c67'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='306718'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=e203f59c6d3a4acc85d63a8ab7352028
+  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=1465381
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.aiHXfwgI/pbuilderrc_2s0X --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aiHXfwgI/b1 --logfile b1/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+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://46.16.76.132:3128'
+  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.aiHXfwgI/pbuilderrc_iCH9 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.aiHXfwgI/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://213.165.73.152:3128
 I: uname -a
-  Linux ionos1-amd64 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.10.11+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.10.11-1~bpo12+1 (2024-10-03) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Aug  4 21:30 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/306718/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Aug  4  2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/1465381/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -257,7 +289,7 @@
 Get: 130 http://deb.debian.org/debian unstable/main amd64 libsprng2-dev amd64 2.0a-16 [78.8 kB]
 Get: 131 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B]
 Get: 132 http://deb.debian.org/debian unstable/main amd64 time amd64 1.9-0.2 [50.8 kB]
-Fetched 136 MB in 9s (15.9 MB/s)
+Fetched 136 MB in 1s (104 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 ... 19968 files and directories currently installed.)
@@ -806,7 +838,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/iqtree-2.0.7+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../iqtree_2.0.7+dfsg-1_source.changes
+I: user script /srv/workspace/pbuilder/1465381/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/1465381/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
@@ -902,8 +938,8 @@
 
 
 -- clang-tidy not found.
--- Configuring done (8.3s)
--- Generating done (0.4s)
+-- Configuring done (2.1s)
+-- Generating done (0.1s)
 CMake Warning:
   Manually-specified variables were not used by the project:
 
@@ -989,8 +1025,8 @@
 
 
 -- clang-tidy not found.
--- Configuring done (5.8s)
--- Generating done (0.5s)
+-- Configuring done (1.3s)
+-- Generating done (0.1s)
 CMake Warning:
   Manually-specified variables were not used by the project:
 
@@ -1079,8 +1115,8 @@
 
 
 -- clang-tidy not found.
--- Configuring done (7.8s)
--- Generating done (0.6s)
+-- Configuring done (2.0s)
+-- Generating done (0.1s)
 CMake Warning:
   Manually-specified variables were not used by the project:
 
@@ -1098,104 +1134,196 @@
    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
+	cd build.omp && make -j42 "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'
-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  -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend
 make  -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend
 make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake "--color="
+make  -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.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/kernelavx.dir/DependInfo.cmake "--color="
+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 /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  -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend
+make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
+make  -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
 make[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/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  -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
+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/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]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-make  -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
-make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
+make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color="
-make  -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake "--color="
+make  -f 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/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 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/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 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/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 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/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color="
+make  -f 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.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]: 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="
+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="
+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[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/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[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/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
+make  -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
+make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
+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 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  -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[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/build
+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[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 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'
-make  -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
-[  0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
-/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.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  -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
+make  -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
+make[4]: Entering directory '/build/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'
+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[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 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'
+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'
 [  0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
-[  0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
 [  1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
+[  1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
+[  1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
+[  1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
 [  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.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 -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
-/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[  3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
-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/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/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
-[  3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.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
+[  2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.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/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
+[  2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.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/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
-[  3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[  3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
+[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
+[  3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
+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
+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
+[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
+[  4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
+[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
+[  4%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
+[  4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.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/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
+[  6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
+[  6%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.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
+/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 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
-[  4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.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/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
+[  8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
+[  9%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o
+[  9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
+[  9%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o
+[  9%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
+[  9%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
+[ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.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
+[ 10%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
+[ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.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/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
-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
-[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
-[  4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
-[  4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
-[  5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.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/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.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
-[  5%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
-[  6%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
-[  6%] 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/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/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
+[ 12%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.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
+[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
+[ 14%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
+[ 14%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
+[ 14%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.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/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/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.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
+[ 14%] 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/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.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
+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
+[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
+[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.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
+[ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.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
+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
+[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
+[ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o
+[ 16%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
+[ 16%] Building C object whtest/CMakeFiles/whtest.dir/eigen.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
+[ 16%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.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/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/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
+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
+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
+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/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
+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
+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
+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
+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
+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/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
+[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.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
+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
+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
+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
 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
 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
-[  6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 16%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
+[ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
+[ 16%] 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
 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
-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
-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
-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
-[  6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
-[  6%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.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
-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
-/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu':
-/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
-   93 |         fscanf (fd, "%d", &id);
-      |         ^~~~~~~~~~~~~~~~~~~~~~
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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/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);
@@ -1207,14 +1335,6 @@
 /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);
-      |                              ^~~~~~~~~~~~~~~
-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/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);
@@ -1235,6 +1355,10 @@
 /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/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);
+      |                              ^~~~~~~~~~~~~~~
 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]
@@ -1260,24 +1384,267 @@
 /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);
       |   ^~~~~~~~~~~~~~~~~~
-[  7%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c: In function 'pll_probe_cpu':
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
+   93 |         fscanf (fd, "%d", &id);
+      |         ^~~~~~~~~~~~~~~~~~~~~~
+[ 17%] 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
+[ 18%] 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
+[ 18%] 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
+[ 18%] 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
+[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
+[ 19%] 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
+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
+[ 19%] 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
+[ 19%] 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
+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
+[ 20%] 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
+[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o
+/usr/bin/ranlib libvectorclass.a
+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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 21%] 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
+[ 22%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o
+[ 22%] Built target vectorclass
+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
+[ 23%] 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
+[ 23%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o
+[ 24%] Linking C static library libsprng.a
+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
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
+[ 24%] 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
+[ 24%] 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
+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
+[ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+/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'
+[ 24%] Built target sprng
+[ 25%] 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
+[ 26%] 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
+[ 26%] 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
+[ 27%] 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
+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
+[ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -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
+/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'
+[ 27%] 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
+[ 27%] Built target gsl
+/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 );
+      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
+[ 28%] 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
+[ 28%] 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
+[ 28%] 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
+[ 29%] 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
+/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);
+      |                                    ~~~~~~^~~~~~~~
+[ 30%] 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
-[  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 pll/CMakeFiles/pll.dir/lexer.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/ncl/nxsdiscretedatum.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/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);
+      |                              ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 30%] 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
+[ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -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
+[ 30%] 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
-[  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
-[  9%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o
+[ 31%] 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
+[ 32%] 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
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+ 1781 |                 cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_function.h:1435:
+/usr/include/c++/14/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+[ 32%] 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
+[ 33%] 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
-[ 10%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
-[ 10%] Building C object pll/CMakeFiles/pll.dir/models.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
+[ 33%] 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
-[ 10%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
+[ 33%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
+[ 34%] 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/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
-[ 10%] 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
+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
+[ 34%] 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
+[ 34%] 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
+[ 34%] 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
+[ 35%] 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
 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);
@@ -1295,22 +1662,36 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign'
  3074 |   rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double));
       |   ^~~~~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53:
+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);
       |                              ^~~~~~~~~~~~~~~
-[ 10%] 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/newick.c:36:
+[ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o
+[ 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
+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
+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);
       |                              ^~~~~~~~~~~~~~~
-[ 10%] 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
-[ 11%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1324,8 +1705,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 12%] 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/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);
@@ -1342,26 +1721,27 @@
 /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);
       |                 ^~~~~~~~~~~~~~~~~~
-[ 12%] 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
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 36%] 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
 /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));
       |           ^~~~~~~~~~~~~~~~~~
-[ 12%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
 /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));
       |   ^~~~~~~~~~~~~~~~~~
-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
-[ 12%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1375,54 +1755,39 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/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);
-      |                              ^~~~~~~~~~~~~~~
-[ 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
-[ 14%] 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
-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
-[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-/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
-[ 16%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/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
-[ 16%] Built target sprng
-[ 16%] 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/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/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);
-      |                              ^~~~~~~~~~~~~~~
+[ 36%] 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/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/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);
+      |                              ^~~~~~~~~~~~~~~
+[ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.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/phylotreeavx.cpp:11:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1432,30 +1797,40 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 16%] Building C object pll/CMakeFiles/pll.dir/queue.c.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
+[ 36%] 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
-[ 17%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o
+[ 37%] 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
-[ 17%] 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
-[ 17%] 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
-[ 17%] Building C object pll/CMakeFiles/pll.dir/recom.c.o
+[ 37%] 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
+[ 38%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
   150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
       |                              ^~~~~~~~~~~~~~~
+[ 39%] Building C object pll/CMakeFiles/pll.dir/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/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);
       |                              ^~~~~~~~~~~~~~~
-[ 18%] 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
-[ 19%] 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
+[ 40%] 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
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o
+[ 40%] 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
+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
+[ 41%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1469,128 +1844,72 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 19%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o
+[ 41%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
- 1781 |                 cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_function.h:1435:
-/usr/include/c++/14/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-[ 19%] 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/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);
-      |                              ^~~~~~~~~~~~~~~
-[ 20%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 20%] 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
-[ 20%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
+[ 41%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 42%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51:
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
+  150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
+      |                              ^~~~~~~~~~~~~~~
+[ 43%] Linking C static library libbooster.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
+/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o
+[ 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
-[ 21%] Building C object pll/CMakeFiles/pll.dir/trash.c.o
+/usr/bin/ranlib libbooster.a
+[ 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
-[ 22%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
+[ 44%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.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
+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
+[ 44%] Built target booster
+[ 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/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
 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 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
 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);
       |                              ^~~~~~~~~~~~~~~
-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="
-[ 22%] 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
-[ 22%] 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
-make[4]: Leaving 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]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
-[ 23%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.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
-/usr/bin/ranlib liblbfgsb.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 23%] Built target lbfgsb
-make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.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/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="
+[ 45%] 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
 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);
       |                              ^~~~~~~~~~~~~~~
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
-[ 23%] 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
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 24%] 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
-[ 24%] 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
-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  -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 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'
-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
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 25%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
-[ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.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
-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
-[ 26%] 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
-[ 26%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
-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="
-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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 27%] 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
-[ 27%] 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
-[ 27%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
+[ 46%] 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
 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);
       |                              ^~~~~~~~~~~~~~~
-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
 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]
@@ -1648,41 +1967,16 @@
 /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) *
       |           ^~~~~~~~~~~~~~~~~~
-[ 27%] 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
-[ 27%] 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
-[ 28%] 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
-[ 28%] 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
-[ 28%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o
-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
-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
-/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
-/usr/bin/ranlib libvectorclass.a
-[ 29%] 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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 29%] Built target vectorclass
-make  -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend
-[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.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 && /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/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
-[ 29%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/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
-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'
-[ 29%] 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
-[ 30%] 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
-[ 31%] 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
+[ 46%] 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
+[ 46%] 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
+[ 47%] 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
+[ 47%] 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/ncl/nxsdatablock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1696,60 +1990,44 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/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);
-      |                                    ~~~~~~^~~~~~~~
-[ 32%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o
-make  -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend
-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
-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="
-[ 32%] 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
-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
-[ 32%] Linking CXX static library libgsl.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1
-/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-/usr/bin/ranlib libgsl.a
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
-[ 32%] Built target gsl
-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
-[ 32%] Building C object whtest/CMakeFiles/whtest.dir/random.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/ncl/nxsdiscretedatum.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 47%] 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
+[ 48%] 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
+[ 49%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1763,33 +2041,33 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 32%] 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
-[ 33%] 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
-[ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o
-[ 34%] 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.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.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
-[ 35%] 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
-[ 35%] 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
-[ 35%] 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
-[ 36%] 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
-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="
-[ 36%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o
+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
+[ 50%] 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
+[ 50%] 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
+/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
+/usr/bin/ranlib libwhtest.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o
+[ 50%] Built target whtest
+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
+[ 51%] 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
+[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o
+[ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
+[ 52%] 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/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
+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
+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
+[ 52%] 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
+[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -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
+[ 53%] 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/ncl/nxsdiscretematrix.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1803,13 +2081,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/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
-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'
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1823,25 +2096,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 36%] 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
-[ 37%] 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 );
-      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
-[ 37%] 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
-[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -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
-[ 37%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1855,8 +2111,10 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 54%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1870,15 +2128,15 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 37%] 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
-[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -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
-[ 38%] 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/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'
+[ 54%] 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
+[ 54%] Built target pllavx
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -1886,89 +2144,87 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 39%] Linking C static library libbooster.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
-[ 40%] 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
-/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
-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
-[ 41%] 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
-/usr/bin/ranlib libbooster.a
+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'
-/usr/bin/ranlib libpll.a
-[ 41%] Built target booster
+[ 54%] Built target lbfgsb
+make  -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake "--color="
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 41%] 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
-[ 41%] Built target pll
-[ 42%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
+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'
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o
+[ 56%] 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/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/utils/gzstream.cpp
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/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
+[ 57%] 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/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 CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.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
+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
+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
+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
+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
+[ 58%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+                 from /usr/include/c++/14/map:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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
+/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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 43%] 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
-[ 44%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 44%] 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
-[ 44%] 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
+[ 58%] 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="
 In 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:
@@ -1986,54 +2242,42 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-[ 44%] Linking CXX static library libterraphast.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake
-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
-/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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-/usr/bin/ranlib libterraphast.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 44%] Built target terraphast
-[ 45%] 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
-[ 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
-[ 45%] 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
-[ 46%] 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
+make  -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 58%] 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
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o
+[ 61%] 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/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
+[ 61%] 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/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
+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
+[ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o
+[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.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
+[ 62%] 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/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
+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
+[ 63%] 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/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
+[ 63%] 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/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.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
+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
+[ 64%] 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/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/pda/graph.cpp
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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
+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
+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/ncl/nxsreader.cpp:19:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2041,96 +2285,59 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-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
-[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o
-/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.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 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
-/usr/bin/ranlib libpllavx.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 47%] Built target pllavx
-[ 48%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 49%] 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
-[ 49%] 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
-[ 49%] 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
-[ 50%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/usr/bin/ar qc 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
-[ 50%] 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'
-[ 50%] Built target whtest
-[ 50%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 51%] 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
-[ 52%] 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
-[ 52%] 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
-[ 52%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2141,7 +2348,7 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2155,25 +2362,26 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 52%] 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/ncl/nxstreesblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2182,32 +2390,29 @@
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
                  from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/sstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 53%] 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
-[ 53%] 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
-[ 53%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/map:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2216,38 +2421,11 @@
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
                  from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/sstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 54%] 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
-[ 55%] 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'
-[ 55%] 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
-[ 55%] Built target nclextra
-make  -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake "--color="
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-make  -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 55%] 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
-[ 56%] 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
-[ 56%] 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
-[ 56%] 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
-[ 56%] 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
 In 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,
@@ -2264,108 +2442,132 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 57%] 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
-[ 57%] 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
-[ 58%] 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
-[ 58%] 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
-[ 58%] 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
-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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 59%] 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
-/usr/bin/ranlib libncl.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 60%] 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
-[ 60%] Built target ncl
-make  -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
-[ 60%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-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
-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'
-[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
-[ 61%] 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
-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
-[ 61%] 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
-[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 62%] 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
-[ 62%] 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/pda/gurobiwrapper.cpp:24:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 63%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 64%] Linking CXX static library libterraphast.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake
+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
+/usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o
+/usr/bin/ranlib libterraphast.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 64%] Built target terraphast
+[ 65%] 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
+/usr/bin/ranlib libpll.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 65%] Built target pll
+[ 66%] 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"
+[ 66%] Linking CXX static library libncl.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1
+/usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o
+/usr/bin/ranlib libncl.a
+/usr/bin/ranlib libyaml-cpp.a
+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'
+[ 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.omp'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+make  -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
+[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
+[ 68%] 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/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
+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
+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
+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
+[ 69%] 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/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
+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
+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
+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
+[ 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 /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,
@@ -2375,28 +2577,37 @@
    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/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -2416,8 +2627,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 63%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -2441,75 +2650,24 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o
-[ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.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
-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
-[ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/phylo-yaml/statespace.h:21,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 64%] 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
-[ 65%] 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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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
-In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -2528,15 +2686,26 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 66%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2546,69 +2715,153 @@
                  from /usr/include/c++/14/ios:44,
                  from /usr/include/c++/14/ostream:40,
                  from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
+[ 69%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 69%] Built target pda
+make  -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color="
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+make  -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 71%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
+[ 71%] 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/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
+[ 71%] 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/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
+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
+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
+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
+[ 71%] Linking CXX static library libutils.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1
+/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
+/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__;
+      |                                                                ^~~~~~~~
+/usr/bin/ranlib libutils.a
+/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
+      |                                                     ^~~~~~~~
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 71%] Built target utils
+make  -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake "--color="
+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'
+[ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
+[ 74%] 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/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
+[ 74%] 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/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.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
+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
+[ 75%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
+[ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o
+[ 76%] 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/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
+[ 76%] 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/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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+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
+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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o
+[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o
+[ 78%] 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/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp
+[ 78%] Building CXX object model/CMakeFiles/model.dir/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/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
+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
+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
+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
+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
+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
+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
+[ 79%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
+[ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o
+[ 80%] 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/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
+[ 80%] 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/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
+[ 80%] 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/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp
+[ 81%] Building CXX object model/CMakeFiles/model.dir/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/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
+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
+[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o
+[ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o
+[ 82%] 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/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
+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
+[ 82%] 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/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
+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
+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
+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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 68%] Building CXX object 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2619,41 +2872,40 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2663,87 +2915,25 @@
 /usr/include/c++/14/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
- 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) {
-      |                                                                                            ^~~~~
-[ 69%] 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/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/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/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/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/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.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
-[ 71%] 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/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
-[ 71%] 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
-[ 72%] 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
-[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
-[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
-[ 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/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.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
-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
-[ 73%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o
-[ 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/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
-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
-[ 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2758,7 +2948,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2772,8 +2963,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2787,9 +2977,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2803,7 +2991,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2817,16 +3005,15 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -2835,8 +3022,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2850,7 +3037,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2861,24 +3048,10 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2904,24 +3077,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -2931,146 +3093,27 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-   69 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  892 | void ModelProtein::readRates(istream &in) throw(const char*, string) {
-      |                                           ^~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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/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*);
-      |                                                ^~~~~
-[ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23:
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/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*);
-      |                                                ^~~~~
-[ 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3080,18 +3123,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 76%] Building CXX object model/CMakeFiles/model.dir/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
-[ 76%] Linking CXX static library libpda.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
-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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3101,17 +3138,15 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 77%] Building CXX object model/CMakeFiles/model.dir/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/ratefreeinvar.cpp.o
-[ 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
-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/ratemeyerhaeseler.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3121,26 +3156,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 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.omp'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake "--color="
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-make  -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 78%] 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
-[ 78%] 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
-/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/ratefree.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3150,17 +3171,23 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 79%] Building CXX object model/CMakeFiles/model.dir/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
-[ 79%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3170,13 +3197,18 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3190,13 +3222,16 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3204,37 +3239,25 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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/modelcodon.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3244,48 +3267,30 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 80%] Building CXX object model/CMakeFiles/model.dir/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
-/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*) {
-      |                                             ^~~~~
-[ 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
-[ 81%] 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/modelmixture.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-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
-/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3295,22 +3300,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/usr/bin/ranlib libphyloYAML.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o
-[ 81%] Built target phyloYAML
-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
-[ 82%] 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
-[ 82%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3320,6 +3315,10 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+ 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) {
+      |                                                                                            ^~~~~
+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);
       |                                             ^~~~~
@@ -3332,6 +3331,15 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   91 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   69 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -3344,15 +3352,15 @@
 /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:
+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/model/modelmixture.cpp:10:
+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/model/modelmixture.cpp:13:
+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);
       |                                             ^~~~~
@@ -3368,46 +3376,18 @@
 /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/modelmarkov.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/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/modelpomomixture.h:14,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h: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);
       |                                             ^~~~~
@@ -3420,29 +3400,21 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 82%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 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
-[ 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
+/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/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -3458,33 +3430,11 @@
 /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/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /usr/include/c++/14/complex:45,
-                 from /usr/include/eigen3/Eigen/Core:50,
-                 from /usr/include/eigen3/Eigen/Dense:1,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
-  927 |             << iqtree_VERSION_PATCH << " built " << __DATE__ << endl
-      |                                                     ^~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/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/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);
       |                                             ^~~~~
@@ -3497,8 +3447,9 @@
 /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/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/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);
       |                                             ^~~~~
@@ -3511,65 +3462,18 @@
 /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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
+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);
       |                                             ^~~~~
@@ -3582,7 +3486,9 @@
 /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/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);
       |                                             ^~~~~
@@ -3595,19 +3501,62 @@
 /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:
+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/main/phylotesting.cpp:31:
+/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: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/main/phylotesting.cpp:34:
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
    78 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37:
+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/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/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);
       |                                             ^~~~~
@@ -3620,14 +3569,70 @@
 /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*);
+      |                                                ^~~~~
+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*);
+      |                                                ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/sstream:40,
+                 from /usr/include/c++/14/complex:45,
+                 from /usr/include/eigen3/Eigen/Core:50,
+                 from /usr/include/eigen3/Eigen/Dense:1,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/main/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 | }
@@ -3636,20 +3641,58 @@
 /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
+/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%] Linking CXX static library libphyloYAML.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1
+/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'
-[ 84%] Built target kernelsse
-[ 85%] Linking CXX static library libmain.a
+[ 83%] Built target phyloYAML
+/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*) {
+      |                                             ^~~~~
+[ 84%] 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
+[ 84%] Built target main
+[ 85%] Linking CXX static library libkernelsse.a
+/usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake
+/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1
+/usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
+/usr/bin/ranlib libkernelsse.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 85%] Built target kernelsse
+[ 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 CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
+/usr/bin/ranlib libalignment.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
+[ 85%] Built target alignment
 [ 86%] Linking CXX static library libkernelfma.a
 /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake
 /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1
@@ -3664,13 +3707,6 @@
 /usr/bin/ranlib libkernelavx.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 [ 86%] Built target kernelavx
-[ 86%] Linking CXX static library libalignment.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
-/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
-/usr/bin/ranlib libalignment.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 86%] Built target alignment
 [ 87%] Linking CXX static library libmodel.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1
@@ -3684,50 +3720,73 @@
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
 make  -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.omp'
-[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
-[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
-[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o
+[ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
+[ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
+[ 88%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
+[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o
+[ 97%] 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/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
+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
+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
 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/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.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/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
 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
-[ 89%] 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/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/mexttree.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/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/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/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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
 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
-[ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
-[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/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/phylosupertreeplen.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
 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
-[ 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/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/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/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp
-[ 94%] Building CXX object tree/CMakeFiles/tree.dir/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/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
-[ 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
-[ 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/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
 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
-[ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o
-[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 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
+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
+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/ncl/ncl.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3741,16 +3800,14 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3769,8 +3826,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3783,8 +3840,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3796,9 +3853,9 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3811,24 +3868,21 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3841,8 +3895,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3855,7 +3909,41 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp:8:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3869,7 +3957,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3883,7 +3971,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3898,9 +3986,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3914,13 +4001,16 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -3941,9 +4031,22 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3958,7 +4061,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3973,8 +4077,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3988,7 +4092,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -3998,26 +4102,21 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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/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);
@@ -4031,21 +4130,8 @@
 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29:
+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);
       |                                             ^~~~~
@@ -4072,23 +4158,7 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12:
+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);
       |                                             ^~~~~
@@ -4101,24 +4171,6 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 /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 | }
@@ -4127,22 +4179,6 @@
 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 [ 98%] Linking CXX static library libtree.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1
@@ -4213,7 +4249,7 @@
 # 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
+	cd build.serial && make -j42 "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
@@ -4222,107 +4258,206 @@
 make  -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend
 make  -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend
 make  -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend
+make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend
+make  -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend
 make[4]: Entering directory '/build/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/kernelsse.dir/DependInfo.cmake "--color="
+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.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  -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.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/kernelfma.dir/DependInfo.cmake "--color="
-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.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/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color="
 make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
 make  -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend
+make  -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend
+make[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/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake "--color="
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake "--color="
-make  -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend
-make[4]: Leaving 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]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake "--color="
+make  -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'
 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]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-make  -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake "--color="
-make[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/depend
+make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake "--color="
+make  -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.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/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'
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color="
+make  -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/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake "--color="
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+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'
+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="
+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[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  -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
+make  -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
+make  -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build
 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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
+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]: 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 terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
-[  1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
+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'
-/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build
+make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
 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.serial'
-make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build
+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.serial'
+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  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-make  -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
+make[4]: Leaving directory '/build/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'
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[  1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
+make  -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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'
-/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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  -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 whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.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/pllavx.dir/build.make pll/CMakeFiles/pllavx.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[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-make  -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build
-[  1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
-[  1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
 make[4]: Entering 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  -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'
+[  0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
+[  0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
+[  1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
+[  1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+[  1%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
+[  2%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o
+[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.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 -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=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
+[  4%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.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/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
+/usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+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
+[  4%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
+[  4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
+[  5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
+[  5%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
+[  5%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
+[  5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
+[  5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
+[  6%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
+[  6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o
+[  6%] 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 -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
+[  7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.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
-[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
-[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
+[  7%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.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/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
+[  7%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
+[  7%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
+[  8%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.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/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
-[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
-[  2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
-[  2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[  2%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
-[  3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.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/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
-[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.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/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 CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
-[  4%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
-[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o
-[  4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.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
+[  8%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
+[  8%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o
+[  8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
+[  9%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o
+[  9%] Building C object booster/CMakeFiles/booster.dir/io.c.o
+[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o
+[ 12%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
+[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
+[ 12%] Building C object booster/CMakeFiles/booster.dir/bitset_index.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/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.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
-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
-[  5%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
-[  6%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.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/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/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
-[  6%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+[ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.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/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/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
-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
+[ 13%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.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
-[  7%] 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/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 gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o
+[ 14%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o
+[ 14%] 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/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.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/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
+[ 14%] 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/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
+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
+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
+[ 15%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.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/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
+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
+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/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
+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
+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
+[ 15%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.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
+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
+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
+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
+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
+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
+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/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
+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/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
+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
+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
+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
 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
-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
+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
+[ 15%] 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
+[ 15%] 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
 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);
       |                              ^~~~~~~~~~~~~~~
-[  7%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 16%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
+[ 16%] 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
+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));
+      |   ^~~~~~~~~~~~~~~~~~
 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/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);
+      |                              ^~~~~~~~~~~~~~~
 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]
@@ -4336,6 +4471,10 @@
 /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);
       |   ^~~~~~~~~~~~~~~~~~
+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);
+      |                              ^~~~~~~~~~~~~~~
 /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
@@ -4348,45 +4487,6 @@
 /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/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));
-      |   ^~~~~~~~~~~~~~~~~~
-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);
-      |                              ^~~~~~~~~~~~~~~
-[  8%] 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
-[  8%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[  9%] 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
-[  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%] 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
-[ 10%] 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
-[ 10%] 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
-/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);
-      |         ^~~~~~~~~~~~~~~~~~~~~~
-[ 10%] 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
-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]
@@ -4399,35 +4499,101 @@
 /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);
       |   ^~~~~~~~~~~~~~~~~~
-[ 11%] Linking C static library libsprng.a
+[ 16%] 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
+[ 17%] 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
+[ 18%] 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
+[ 18%] 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
+[ 19%] 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
+[ 20%] Linking CXX static library libvectorclass.a
+[ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
+[ 21%] Linking C static library libsprng.a
+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
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
-[ 11%] 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
+[ 22%] 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
+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
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1
+/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
+[ 22%] 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
 /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 libvectorclass.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o
+[ 23%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
 /usr/bin/ranlib libsprng.a
-[ 12%] 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
+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
+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
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 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
-[ 13%] Built target sprng
-make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.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/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="
-[ 13%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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
+[ 24%] 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
+[ 24%] Built target sprng
+[ 24%] Built target vectorclass
+[ 25%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
+[ 25%] 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/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
+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
+[ 25%] 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
+/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);
+      |         ^~~~~~~~~~~~~~~~~~~~~~
+[ 25%] Linking CXX static library libgsl.a
+[ 25%] Building C object booster/CMakeFiles/booster.dir/prng.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake
+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
+[ 26%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o
+/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);
+      |                                    ~~~~~~^~~~~~~~
+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
+/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);
+      |                                    ~~~~~~^~~~~~~~
+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
+[ 26%] 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
+/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
+[ 27%] 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
+[ 27%] 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
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
-[ 13%] Building C object pll/CMakeFiles/pll.dir/models.c.o
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 28%] 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
+[ 28%] Built target gsl
+[ 28%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o
+[ 28%] 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
+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
+[ 28%] 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
+[ 29%] 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
+[ 29%] 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
-[ 14%] Building C object booster/CMakeFiles/booster.dir/bitset_index.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
 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);
       |                              ^~~~~~~~~~~~~~~
+[ 29%] 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
 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]
@@ -4435,22 +4601,25 @@
 /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));
       |   ^~~~~~~~~~~~~~~~~~
+[ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT':
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result]
    39 |     #define rax_posix_memalign posix_memalign
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign'
  3074 |   rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double));
       |   ^~~~~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/models.c:53:
-/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
-  150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
-      |                              ^~~~~~~~~~~~~~~
-[ 15%] 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
-[ 15%] 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
+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/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 );
+      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
+[ 30%] 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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4465,7 +4634,8 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4479,113 +4649,21 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 15%] 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
-[ 15%] 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
-[ 15%] 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
-[ 15%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 16%] 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
-[ 17%] 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
-[ 18%] 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
-[ 18%] 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
-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));
-      |   ^~~~~~~~~~~~~~~~~~
-[ 19%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 19%] 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
-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
-[ 19%] 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
-/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'
-[ 19%] Built target gsl
-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'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake "--color="
-make[4]: 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'
-[ 20%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
-[ 20%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.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
-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
-[ 21%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 21%] 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
-[ 21%] Linking CXX static library libvectorclass.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1
-/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'
-[ 21%] 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.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/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 nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 22%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -4601,58 +4679,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 22%] 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
-[ 23%] 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
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
- 1781 |                 cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t));
-      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_function.h:1435:
-/usr/include/c++/14/backward/binders.h:172:5: note: declared here
-  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
-      |     ^~~~~~~
-[ 24%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend
-[ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /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="
-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
-[ 24%] 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
-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
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 24%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4666,80 +4694,20 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 25%] 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
-[ 25%] 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
-[ 25%] 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
-/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);
-      |                                    ~~~~~~^~~~~~~~
-[ 25%] 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
-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
-[ 26%] 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
-/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'
-[ 26%] 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.serial'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake "--color="
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
+[ 30%] 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
+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);
       |                              ^~~~~~~~~~~~~~~
-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'
-[ 26%] 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
+[ 31%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 26%] 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
-[ 26%] 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
-[ 27%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 27%] 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
-[ 28%] 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/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -4755,143 +4723,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 28%] 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
-[ 28%] 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
-[ 29%] 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
-[ 29%] 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
-[ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 31%] Building C object pll/CMakeFiles/pll.dir/stack.c.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
-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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 31%] 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
-[ 32%] 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
-[ 32%] 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
-[ 33%] 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
-[ 33%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 33%] 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
-[ 34%] 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 );
-      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
-[ 34%] 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
-[ 34%] 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
-[ 35%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 35%] 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
-[ 35%] 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
-[ 35%] 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
-[ 35%] 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
-[ 35%] 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/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);
-      |                              ^~~~~~~~~~~~~~~
-[ 36%] 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
-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) *
-      |           ^~~~~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
@@ -4902,36 +4733,15 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-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="
-[ 37%] Linking C static library libbooster.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
-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'
-/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
-[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.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/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
-[ 37%] Built target booster
-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'
-[ 37%] 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
-[ 38%] 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
-[ 38%] 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/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);
+      |                              ^~~~~~~~~~~~~~~
+[ 31%] 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/nclextra/msetsblock.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4945,8 +4755,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/newick.c:36:
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
+  150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
+      |                              ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4960,26 +4775,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 39%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -4993,9 +4790,22 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp: In member function 'virtual unsigned int NxsCharactersBlock::HandleTokenState(NxsToken&, unsigned int)':
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:1781:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NxsStringEqual; _Tp = NxsString]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations]
+ 1781 |                 cit = find_if (ci_begin, ci_end, bind2nd(NxsStringEqual(), t));
+      |                                                  ~~~~~~~^~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_function.h:1435:
+/usr/include/c++/14/backward/binders.h:172:5: note: declared here
+  172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
+      |     ^~~~~~~
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 32%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5003,20 +4813,34 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 40%] Building CXX object 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
-[ 40%] 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
+[ 32%] 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
+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);
+      |                 ^~~~~~~~~~~~~~~~~~
+[ 32%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5030,9 +4854,24 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 32%] 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
+/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));
+      |   ^~~~~~~~~~~~~~~~~~
+[ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5040,20 +4879,23 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 40%] Building CXX object 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47:
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
+  150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
+      |                              ^~~~~~~~~~~~~~~
+[ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.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/nxsdistancesblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
+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 /usr/include/c++/14/string:49,
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
@@ -5064,25 +4906,37 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-[ 42%] 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
-[ 43%] 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
-[ 43%] 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
-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
-[ 43%] 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
+[ 33%] 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
+[ 33%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/parsePartition.c:42:
+/build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
+  150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
+      |                              ^~~~~~~~~~~~~~~
+[ 34%] Building 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
+[ 35%] 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
+[ 35%] 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
+[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o
+[ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o
+[ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.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
+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
+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
+[ 38%] 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
+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/ncl/nxsemptyblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 In file included from /usr/include/c++/14/string:49,
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
@@ -5093,57 +4947,40 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 43%] Built target pll
-[ 43%] 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
-[ 44%] 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'
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 44%] Built target pllavx
-[ 44%] 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
-[ 45%] 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
-[ 45%] 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
-/usr/bin/ranlib libwhtest.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/tools.cpp:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 45%] Built target whtest
-[ 46%] 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
+[ 38%] 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
+[ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o
+[ 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
+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
+[ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 39%] 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
+[ 39%] 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
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.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/modelsblock.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5157,31 +4994,53 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 46%] 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
-/usr/bin/ranlib libterraphast.a
-[ 46%] 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
-[ 46%] 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
+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
+[ 39%] 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
+[ 40%] 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/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 40%] 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
+[ 40%] 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
+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%] Building C object pll/CMakeFiles/pll.dir/trash.c.o
+[ 42%] Building C object pll/CMakeFiles/pll.dir/stack.c.o
+[ 42%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
+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);
+      |                              ^~~~~~~~~~~~~~~
+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
+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
+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
+[ 43%] 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
+[ 43%] 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
+[ 44%] 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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5195,28 +5054,43 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/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 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
+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
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 45%] 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
+/usr/bin/ranlib libbooster.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 46%] Built target terraphast
-[ 47%] 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
-[ 48%] 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
-[ 48%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5230,27 +5104,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 45%] 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
+[ 45%] Built target booster
+[ 45%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/map:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 48%] 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
-[ 49%] 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
-[ 50%] 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
-In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5264,61 +5124,220 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 46%] 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
+[ 46%] 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/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) *
+      |           ^~~~~~~~~~~~~~~~~~
+[ 47%] 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 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
+[ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
+[ 48%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 50%] 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
-[ 50%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 51%] Linking CXX static library libnclextra.a
+[ 48%] 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
+[ 48%] 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
+[ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
+[ 49%] 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
+[ 50%] 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
+[ 50%] 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
+[ 51%] 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
+[ 51%] 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
+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
+[ 52%] 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
+[ 52%] 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
+[ 53%] 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
+/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
+[ 53%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 53%] Built target whtest
+[ 53%] 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
+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
+[ 54%] 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
+/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+/usr/bin/ranlib liblbfgsb.a
+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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o
+[ 54%] Built target lbfgsb
+/usr/bin/ranlib libpllavx.a
+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[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'
+[ 54%] Built target pllavx
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
+[ 55%] 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/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
+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
+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
+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
+[ 55%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o
+[ 56%] 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
+[ 57%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o
+[ 57%] 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/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
+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
+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
+[ 58%] Linking CXX static library libnclextra.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1
 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o
 /usr/bin/ranlib libnclextra.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 51%] Built target nclextra
+[ 58%] 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="
-[ 52%] 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
 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'
-[ 52%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
+[ 59%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o
+[ 59%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o
+[ 59%] 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/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
+[ 59%] 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
+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
+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
+[ 59%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 60%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 60%] 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
+[ 61%] 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
+[ 61%] 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
+[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
+[ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o
+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
+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
+[ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o
+[ 63%] 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
+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
+[ 63%] 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
+[ 64%] 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/ncl/nxstoken.cpp:19:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:26:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5326,22 +5345,29 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp:21:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 52%] 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
-[ 53%] 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
-[ 53%] 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
-[ 53%] 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/nxstreesblock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5349,93 +5375,64 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 54%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
-[ 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.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
-[ 55%] 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
-[ 55%] 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
-[ 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.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
-[ 56%] 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
-[ 57%] 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
-[ 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
-[ 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
-[ 58%] 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
-[ 58%] 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
-[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
-[ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
-[ 59%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/map:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 60%] 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
-[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 In 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,
@@ -5449,29 +5446,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 61%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o
-[ 61%] Linking CXX static library libncl.a
-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
-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
-[ 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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 61%] 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'
-[ 61%] 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/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5481,20 +5461,6 @@
 /usr/include/c++/14/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
-[ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -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
-[ 62%] 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
-[ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -5513,29 +5479,22 @@
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-[ 65%] 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
-[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5543,9 +5502,22 @@
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/sstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5563,14 +5535,19 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/boost/math/special_functions/detail/round_fwd.hpp:11,
-                 from /usr/include/boost/math/special_functions/math_fwd.hpp:29,
-                 from /usr/include/boost/math/special_functions/beta.hpp:13,
-                 from /usr/include/boost/math/distributions/binomial.hpp:83,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:22:
-/usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
-   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
-      |      ^~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
@@ -5603,21 +5580,6 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -5633,14 +5595,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 66%] 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/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/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5650,57 +5610,79 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
-cd /build/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
-[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 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/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 64%] 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
+/usr/bin/ranlib libterraphast.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 64%] Built target terraphast
+[ 65%] 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'
+[ 65%] Built target pll
+[ 65%] 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'
+[ 65%] 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'
+[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
+[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
+[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
+[ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
+[ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
+[ 66%] 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/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
+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
+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/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
+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
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 [ 68%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5730,13 +5712,19 @@
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5746,8 +5734,7 @@
                  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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5778,6 +5765,43 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.h:23:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 [ 69%] 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
@@ -5793,46 +5817,18 @@
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 [ 69%] 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
-[ 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="
-/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) {
-      |                                                                                            ^~~~~
-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'
-[ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
-[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
-[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
-[ 70%] 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/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.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
-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
-[ 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/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
-[ 71%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/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
-[ 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/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/partitionmodelplen.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/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
-[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/rategamma.cpp.o
-[ 73%] 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/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
-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
-[ 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/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/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
@@ -5850,13 +5846,58 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 69%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 69%] 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'
+[ 71%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
+[ 71%] 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/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
+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
+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
+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
+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/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+  232 |     out    << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__;
+      |                                                                ^~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+  927 |             << iqtree_VERSION_PATCH << " built " << __DATE__ << endl
+      |                                                     ^~~~~~~~
+/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/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5868,13 +5909,14 @@
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5882,19 +5924,21 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5904,9 +5948,130 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+[ 71%] 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'
+[ 71%] Built target utils
+make  -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.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'
+[ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o
+[ 72%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
+[ 72%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
+[ 72%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o
+[ 73%] 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/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/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
+[ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
+[ 74%] 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/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
+[ 75%] 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/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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
+[ 76%] 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/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
+[ 76%] 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/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
+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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o
+[ 77%] 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/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
+[ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o
+[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o
+[ 78%] 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/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
+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/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
+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
+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
+[ 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/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
+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
+[ 79%] 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/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
+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
+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
+[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
+[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
+[ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o
+[ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o
+[ 81%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o
+[ 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/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
+[ 82%] 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/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
+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
+[ 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/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
+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
+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
+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
+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
+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/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/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/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:34:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   78 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   69 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5914,17 +6079,13 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5932,8 +6093,9 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5947,8 +6109,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5962,7 +6123,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -5976,16 +6137,15 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -5993,7 +6153,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6023,9 +6183,9 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6035,143 +6195,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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*);
-      |                                                ^~~~~
-/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/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) {
-      |                                           ^~~~~
-/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/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
-/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/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*);
-      |                                                ^~~~~
-[ 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6181,13 +6211,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 76%] Building CXX object model/CMakeFiles/model.dir/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6201,7 +6231,9 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6215,7 +6247,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6225,8 +6257,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 76%] Building CXX object model/CMakeFiles/model.dir/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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -6241,32 +6271,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 77%] Building CXX object model/CMakeFiles/model.dir/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
-[ 77%] 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
-[ 77%] 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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 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.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'
-[ 78%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6276,16 +6287,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-/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/rateheterotachy.cpp:9:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelbin.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6295,45 +6303,23 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:13:
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 79%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
-[ 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/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
-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/main/main.cpp:37:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6343,59 +6329,18 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
- 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) {
-      |                                          ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
- 1468 | void ModelMarkov::readRates(string str) throw(const char*) {
-      |                                         ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
- 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) {
-      |                                              ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
- 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) {
-      |                                             ^~~~~
-[ 80%] 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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 80%] 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
-[ 80%] 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
-/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6409,8 +6354,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6425,8 +6370,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6436,87 +6380,20 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 81%] Building CXX object model/CMakeFiles/model.dir/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.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) {
-      |                                              ^~~~~
-[ 81%] 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
-[ 81%] 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
-[ 82%] 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
-/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/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
-  927 |             << iqtree_VERSION_PATCH << " built " << __DATE__ << endl
-      |                                                     ^~~~~~~~
-[ 82%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -6525,8 +6402,10 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6540,11 +6419,9 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6558,22 +6435,15 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /usr/include/c++/14/complex:45,
-                 from /usr/include/eigen3/Eigen/Core:50,
-                 from /usr/include/eigen3/Eigen/Dense:1,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -6581,7 +6451,10 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6591,12 +6464,20 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 83%] Linking CXX static library libphyloYAML.a
+/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 | }
+      | ^
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6606,8 +6487,18 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/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
+/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);
       |                                             ^~~~~
@@ -6623,40 +6514,71 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
    91 |         virtual void readRates(string str) throw(const char*);
       |                                            ^~~~~
-/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-/usr/bin/ranlib libphyloYAML.a
-[ 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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 83%] Built target phyloYAML
+/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.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: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: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: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/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/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  892 | void ModelProtein::readRates(istream &in) throw(const char*, string) {
+      |                                           ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   78 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) {
+      |                                              ^~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -6669,22 +6591,6 @@
 /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/timetree.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/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);
       |                                             ^~~~~
@@ -6697,7 +6603,6 @@
 /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: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);
       |                                             ^~~~~
@@ -6710,15 +6615,34 @@
 /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/modelmarkov.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/main/phylotesting.cpp:21:
+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/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);
       |                                             ^~~~~
@@ -6731,40 +6655,159 @@
 /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:
+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/main/phylotesting.cpp:31:
+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/main/phylotesting.cpp:34:
+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/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
+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/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:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  146 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  153 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  160 |         virtual void readStateFreq(istream &in) throw(const char*);
+      |                                                 ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  167 |         virtual void readStateFreq(string str) throw(const char*);
+      |                                                ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   91 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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*);
+      |                                                ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/sstream:40,
+                 from /usr/include/c++/14/complex:45,
+                 from /usr/include/eigen3/Eigen/Core:50,
+                 from /usr/include/eigen3/Eigen/Dense:1,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.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%] Linking CXX static library libphyloYAML.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1
+/usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o
+/usr/bin/ranlib libphyloYAML.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 84%] Built target kernelsse
-[ 85%] Linking CXX static library libmain.a
+[ 83%] Built target phyloYAML
+/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*) {
+      |                                             ^~~~~
+[ 84%] Linking CXX static library libmain.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1
 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o
 /usr/bin/ranlib libmain.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 85%] Built target main
+[ 84%] Built target main
+[ 85%] Linking CXX static library libkernelsse.a
+/usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake
+/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1
+/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'
+[ 85%] Built target kernelsse
+[ 85%] Linking CXX static library libalignment.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
+/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
+/usr/bin/ranlib libalignment.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
+[ 85%] Built target alignment
 [ 86%] Linking CXX static library libkernelfma.a
 /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake
 /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1
@@ -6772,20 +6815,13 @@
 /usr/bin/ranlib libkernelfma.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 [ 86%] Built target kernelfma
-[ 86%] Linking CXX static library libalignment.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake
 [ 86%] Linking CXX static library libkernelavx.a
 /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
 /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1
-/usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
 /usr/bin/ranlib libkernelavx.a
-/usr/bin/ranlib libalignment.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 [ 86%] Built target kernelavx
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 86%] Built target alignment
 [ 87%] Linking CXX static library libmodel.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1
@@ -6799,49 +6835,59 @@
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
 make  -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.serial'
-[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
-[ 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
-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/iqtree.cpp.o
+[ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
+[ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
 [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o
-[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
 [ 89%] 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/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp
+[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
 [ 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/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
+[ 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/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
+[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.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/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
+[ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/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.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
+[ 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/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp
-[ 91%] Building CXX object tree/CMakeFiles/tree.dir/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/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
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o
-[ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
-[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
+[ 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/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
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
-[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 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
-[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
-[ 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/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp
-[ 95%] Building CXX object tree/CMakeFiles/tree.dir/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/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
-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
 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
-[ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o
+[ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o
+[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
+[ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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/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
+[ 95%] 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/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
+[ 96%] 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/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
+[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
+[ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
+[ 96%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o
+[ 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/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
+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
+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
+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
+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/node.cpp:22:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6867,9 +6913,63 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6885,8 +6985,7 @@
                  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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6900,6 +6999,20 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -6914,13 +7027,17 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -6928,27 +7045,30 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -6956,13 +7076,15 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -6970,7 +7092,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6982,8 +7104,9 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -6995,9 +7118,7 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7009,24 +7130,23 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7039,8 +7159,9 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7054,7 +7175,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7069,8 +7190,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7080,8 +7201,6 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/reproducible-path/iqtree-2.0.7+dfsg -I/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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -7103,7 +7222,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7113,7 +7232,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35:
+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);
       |                                             ^~~~~
@@ -7126,40 +7246,6 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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/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);
@@ -7173,8 +7259,7 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.h:13,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34:
+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);
       |                                             ^~~~~
@@ -7188,7 +7273,7 @@
   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:
+                 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);
       |                                             ^~~~~
@@ -7201,39 +7286,6 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   167 |         virtual void readStateFreq(string str) throw(const char*);
       |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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
 /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 | }
@@ -7242,22 +7294,6 @@
 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 [ 98%] Linking CXX static library libtree.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1
@@ -7328,7 +7364,7 @@
 # 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
+	cd build.mpi && make -j42 "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
@@ -7336,118 +7372,215 @@
 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[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="
+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 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/kernelavx.dir/DependInfo.cmake "--color="
 make  -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend
 make  -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend
 make[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="
+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  -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'
-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="
+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 gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.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/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  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend
+make  -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend
+make[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]: 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/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[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-make  -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
+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/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="
-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.mpi'
-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.mpi'
-make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
+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/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 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/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="
+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/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]: 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/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]: 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]: 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]: 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[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]: 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]: 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 CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build
+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]: 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 CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build
+make  -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+make  -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build
 make[4]: Entering directory '/build/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  -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.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
-[  0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.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 -g -O2 -ffile-prefix-map=/build/reproducible-path/iqtree-2.0.7+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-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  -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'
+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 gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[  0%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
+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  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
+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.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'
-make  -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build
-make  -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build
+make  -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-make  -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend
-[  1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.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/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp
+make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build
+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'
-make  -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.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 -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
 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/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]: 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/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]: 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]: 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 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'
+[  1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o
+[  1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
+[  1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o
+[  1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o
 [  1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
+[  1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
+[  1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o
+[  3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
+[  3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
+[  3%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
+[  4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o
+[  4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
+[  4%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+[  4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/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
+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
+/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
 /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
-[  1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o
-[  2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o
-[  2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.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
-[  2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.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
+/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
+[  4%] Building C object sprng/CMakeFiles/sprng.dir/memory.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/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
+[  5%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o
+[  6%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o
+[  5%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.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/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
-[  2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.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/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
-[  3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
-[  4%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.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/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp
-[  4%] Building 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/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
-[  5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.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
-[  5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o
-[  5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+[  6%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
+[  6%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o
+[  7%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
+[  9%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.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
-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
-[  6%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o
-make  -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build
-[  6%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
-[  6%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o
+[  9%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.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/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.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
-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
-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
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 10%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.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/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
+[ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.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
 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
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-make  -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build
-[  7%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
-make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.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
+[ 11%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o
+[ 13%] Building C object booster/CMakeFiles/booster.dir/io.c.o
+[ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o
+[ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o
+[ 13%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.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
+[ 14%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.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
+[ 16%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
+[ 16%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o
+[ 16%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o
+[ 16%] Building C object booster/CMakeFiles/booster.dir/sort.c.o
+[ 16%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o
+[ 17%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o
+[ 17%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.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
+[ 17%] Building C object whtest/CMakeFiles/whtest.dir/eigen.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
+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
+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/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
+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
 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
-[  8%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.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
+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
+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
+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
+[ 17%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o
+[ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.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
+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
+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
+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
+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
+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
+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
 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
-[  9%] 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
+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
+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
+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
+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
+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
+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
+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
+/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/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/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/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);
@@ -7459,38 +7592,88 @@
 /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 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/alignment.c:40:
+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 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 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
-[ 10%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o
+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);
+      |   ^~~~~~~~~~~~~~~~~~
+[ 17%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
+[ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.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/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/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
+[ 18%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o
+[ 19%] 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/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
+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
+[ 19%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o
+[ 19%] Linking CXX static library libvectorclass.a
+[ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o
+[ 19%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.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/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
+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
+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/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
+[ 19%] 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
+[ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o
+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
+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
+[ 20%] 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
-[ 11%] 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
-[ 11%] Building C object booster/CMakeFiles/booster.dir/tree.c.o
-make  -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend
+[ 21%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+[ 21%] 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 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
-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="
+/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'
-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'
-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="
-[ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o
+[ 21%] 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
-[ 12%] 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
+[ 21%] Built target vectorclass
+[ 22%] 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
+[ 22%] 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
+[ 23%] 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
+[ 23%] 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
+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
+[ 24%] 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
+/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
+[ 24%] 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
+[ 25%] 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
+/usr/bin/ranlib libsprng.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
+[ 26%] Built target sprng
+[ 27%] 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
+[ 27%] 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
+[ 27%] 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
 /build/reproducible-path/iqtree-2.0.7+dfsg/booster/booster.c: In function 'main_booster':
+[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o
 /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);
       |                                                         ^~~~~~~~~~
@@ -7504,48 +7687,13 @@
 /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);
       |                                    ~~~~~~^~~~~~~~
-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'
-[ 13%] Linking C static library libsprng.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake
-[ 13%] 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
-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
-[ 13%] 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
-/usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o "CMakeFiles/sprng.dir/primes-lcg64.c.o" CMakeFiles/sprng.dir/checkid.c.o
-cd /build/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/ranlib libsprng.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 13%] 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
-/usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o
-[ 13%] Built target sprng
-/usr/bin/ranlib libvectorclass.a
-make  -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend
-[ 13%] 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
-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'
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 13%] 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
-[ 13%] Built target vectorclass
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 14%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o
-[ 14%] 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/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
-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
+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
+[ 28%] 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
+[ 28%] 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/nclextra/mpdablock.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7559,68 +7707,55 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 15%] 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
-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);
-      |   ^~~~~~~~~~~~~~~~~~
-[ 15%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o
-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);
-      |                              ^~~~~~~~~~~~~~~
-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
-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);
-      |   ^~~~~~~~~~~~~~~~~~
-[ 16%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 16%] Linking CXX static library libgsl.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/ncl/nxsdiscretematrix.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
+[ 28%] 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
-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
-[ 16%] 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
-/usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o
-/usr/bin/ranlib libgsl.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 16%] Built target gsl
-[ 16%] 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/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
@@ -7636,18 +7771,47 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+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/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);
       |                              ^~~~~~~~~~~~~~~
-[ 17%] 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
-[ 18%] 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
-[ 18%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7661,16 +7825,8 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 19%] 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
-[ 20%] 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
-[ 20%] 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
-[ 20%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7684,12 +7840,10 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/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);
-      |         ^~~~~~~~~~~~~~~~~~~~~~
-[ 21%] Building C object pll/CMakeFiles/pll.dir/hash.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+[ 28%] 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
+/usr/bin/ranlib libgsl.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
 /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));
@@ -7698,62 +7852,226 @@
 /usr/include/c++/14/backward/binders.h:172:5: note: declared here
   172 |     bind2nd(const _Operation& __fn, const _Tp& __x)
       |     ^~~~~~~
-[ 21%] 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
-[ 22%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o
+[ 28%] Built target gsl
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 28%] 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
+[ 29%] 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
+[ 29%] 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
+[ 30%] 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
+[ 30%] 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
+[ 31%] 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
+[ 32%] 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
-[ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o
+[ 32%] 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
+[ 32%] 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
+[ 33%] 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
+[ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/ncl/nxsdistancesblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 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);
       |                              ^~~~~~~~~~~~~~~
-[ 22%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29:
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCAT':
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
 /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));
       |   ^~~~~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function 'coreGTRCATPROT':
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of 'posix_memalign' declared with attribute 'warn_unused_result' [-Wunused-result]
    39 |     #define rax_posix_memalign posix_memalign
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro 'rax_posix_memalign'
  3074 |   rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double));
       |   ^~~~~~~~~~~~~~~~~~
-[ 22%] Building 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
-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 C object booster/CMakeFiles/booster.dir/tree_utils.c.o
+[ 33%] 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
+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
+[ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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
 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 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
-[ 23%] 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
-[ 24%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o
+[ 33%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp:19:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 35%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp:8:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 35%] 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 37%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o
+[ 37%] 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
+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
+[ 38%] 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
+[ 38%] 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
+/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 );
+      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
+[ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
+[ 39%] 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
+[ 39%] 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
+[ 39%] Building C object pll/CMakeFiles/pll.dir/newick.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+[ 40%] 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
-[ 24%] 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
-[ 25%] 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
-[ 25%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o
+[ 40%] 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
+[ 40%] 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
+[ 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
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
-/usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o
-/usr/bin/ranlib libbooster.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 40%] 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/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);
       |                              ^~~~~~~~~~~~~~~
-[ 25%] Built target booster
 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]
@@ -7766,25 +8084,10 @@
 /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);
       |                 ^~~~~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernel.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp:11:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 26%] 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
-[ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
+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);
+      |                              ^~~~~~~~~~~~~~~
 /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
@@ -7797,35 +8100,80 @@
 /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));
       |   ^~~~~~~~~~~~~~~~~~
+[ 41%] Linking C static library libbooster.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1
+[ 41%] 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
+[ 42%] 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
+/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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/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);
-      |                              ^~~~~~~~~~~~~~~
+/usr/bin/ranlib libbooster.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o
+[ 43%] Built target booster
+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
+[ 44%] 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
+[ 44%] 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/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp:19:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/fstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+[ 45%] 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
+[ 45%] 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
+[ 45%] 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
+[ 45%] 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
 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);
       |                              ^~~~~~~~~~~~~~~
-[ 27%] 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
-[ 28%] 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
-[ 28%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
@@ -7841,132 +8189,87 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/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
-[ 28%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 29%] 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
-/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'
-[ 29%] Built target pllavx
-[ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o
-[ 30%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.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
-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
-[ 31%] 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
-[ 31%] 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
-[ 31%] 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
-[ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o
-[ 31%] 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
-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/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);
       |                              ^~~~~~~~~~~~~~~
-[ 31%] 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
-[ 31%] 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
-[ 32%] 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
-[ 32%] 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
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 33%] 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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 33%] 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
-[ 33%] 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
+[ 46%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o
+[ 46%] 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/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
+[ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.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
+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
+[ 47%] 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);
       |                              ^~~~~~~~~~~~~~~
-[ 34%] 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
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1
-/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
-/usr/bin/ranlib liblbfgsb.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 35%] 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
-[ 35%] 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="
-[ 35%] 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/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.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/restartHashTable.c:47:
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/pll/randomTree.c:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined
   150 | extern __inline unsigned int bitcount_64_bit(uint64_t i);
       |                              ^~~~~~~~~~~~~~~
-[ 35%] Building 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
-[ 36%] 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
-/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 );
-      |                         ^~~~~~~~~~~~~~~~~~~~~~~~
-[ 36%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o
+[ 47%] 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
+[ 47%] 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
+[ 48%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 37%] Building C object pll/CMakeFiles/pll.dir/stack.c.o
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 49%] 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
-[ 37%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o
+[ 49%] 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
+[ 49%] 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
+[ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o
+[ 50%] 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/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
+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
+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);
+      |                              ^~~~~~~~~~~~~~~
+[ 50%] 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
+[ 51%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -7980,24 +8283,26 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 51%] 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
+[ 52%] 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 /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);
       |                              ^~~~~~~~~~~~~~~
-[ 38%] 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
 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);
       |                              ^~~~~~~~~~~~~~~
-[ 38%] 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
-[ 38%] 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
-[ 38%] Building C object pll/CMakeFiles/pll.dir/utils.c.o
+[ 52%] 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
-[ 39%] 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
+[ 52%] 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
+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/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);
@@ -8059,12 +8364,92 @@
 /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) *
       |           ^~~~~~~~~~~~~~~~~~
-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);
-      |                              ^~~~~~~~~~~~~~~
-[ 39%] 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
+[ 53%] 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
+/usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o
+/usr/bin/ranlib libpllavx.a
+[ 53%] Linking CXX static library liblbfgsb.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1
+/usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o
+/usr/bin/ranlib liblbfgsb.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 54%] 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
+[ 54%] Built target pllavx
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+/usr/bin/ranlib libnclextra.a
+[ 54%] 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="
+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'
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o
+[ 56%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o
+[ 56%] 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/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
+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
+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
+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
+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
+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
+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
+[ 57%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 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.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'
+[ 57%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o
+[ 57%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o
+[ 57%] 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
+[ 57%] 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/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
+[ 58%] 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/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
+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
+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
+[ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o
+[ 59%] 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/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
+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
+[ 60%] 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
+[ 61%] Linking CXX static library libwhtest.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake
+[ 61%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+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
+[ 62%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
+/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
+[ 62%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 62%] 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
+[ 62%] Built target whtest
+[ 63%] 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
+[ 63%] 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
+[ 64%] 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
 In 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:
@@ -8083,287 +8468,188 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:18:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 39%] 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
-[ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o
-[ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.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
-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
-[ 40%] 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
-[ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o
-[ 41%] 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/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:18,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/map:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 41%] 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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
                  from /usr/include/c++/14/bits/locale_classes.h:40,
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 42%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.cpp:25:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/greedy.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 43%] 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
-[ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.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/nxssetreader.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-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
 In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 44%] 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
-[ 44%] 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
-[ 44%] 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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/pllnni.cpp:34:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 45%] 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'
-[ 45%] 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
-[ 45%] Built target pll
-[ 46%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.h:25,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 47%] 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
-[ 48%] 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
-[ 48%] 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
-[ 48%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pruning.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 48%] 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
-[ 49%] Linking CXX static library libwhtest.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1
-/usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o
-/usr/bin/ranlib libwhtest.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 49%] Built target whtest
-[ 50%] 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
-[ 50%] 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
-[ 50%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/optimization.cpp:12:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/stoprule.cpp:20:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-[ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8372,18 +8658,27 @@
                  from /usr/include/c++/14/bits/ios_base.h:41,
                  from /usr/include/c++/14/ios:44,
                  from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /usr/include/c++/14/sstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:26,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.cpp:22:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8398,24 +8693,26 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 52%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8426,95 +8723,79 @@
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/map:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/checkpoint.h:12:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/sstream:40,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -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
-[ 53%] 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
-[ 53%] 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
-[ 53%] Linking CXX static library libterraphast.a
+[ 64%] 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
+[ 65%] 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/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1
+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 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/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
 /usr/bin/ranlib libterraphast.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 53%] Built target terraphast
-[ 54%] 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
-[ 54%] 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
-[ 55%] 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
-[ 56%] 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
-[ 56%] 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
-[ 56%] Linking CXX static library libncl.a
+[ 65%] 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
-[ 56%] 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
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
 /usr/bin/ranlib libncl.a
-[ 57%] 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
+[ 65%] Built target pll
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 65%] Built target terraphast
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 57%] Built target ncl
+[ 66%] 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"
+[ 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.mpi'
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/iqtree-2.0.7+dfsg /build/reproducible-path/iqtree-2.0.7+dfsg/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake "--color="
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
 make  -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o
+[ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o
+[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o
+[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o
+[ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o
+[ 69%] 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/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
 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
-[ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp:5:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-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
-In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/MPIHelper.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 58%] 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
-[ 59%] 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
-[ 59%] 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
-/usr/bin/ranlib libnclextra.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 59%] 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="
-[ 59%] 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
-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'
-[ 59%] 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
+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
+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
+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
+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
+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 /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)"
+      |      ^~~~~~~
+/usr/bin/ranlib libyaml-cpp.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/phylo-yaml/statespace.h:21,
@@ -8533,34 +8814,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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 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
-[ 61%] 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 /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)"
-      |      ^~~~~~~
-[ 61%] 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 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
-[ 61%] 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
-[ 62%] 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8577,31 +8837,11 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/pdnetwork.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 63%] 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
-[ 63%] 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
-In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8616,8 +8856,8 @@
                  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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/maalignment.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8630,15 +8870,18 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.h:12,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -8647,8 +8890,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8665,38 +8907,31 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:24:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp:23:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/pattern.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignment.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 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
 In 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:
@@ -8709,52 +8944,144 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 64%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/ostream:40,
+                 from /usr/include/c++/14/iostream:41,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+[ 69%] Linking CXX static library libpda.a
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1
+/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
+/usr/bin/ranlib libpda.a
+[ 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
+/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) {
+      |                                                                                            ^~~~~
+/usr/bin/ranlib libutils.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 69%] Built target pda
+make  -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.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'
+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'
+[ 70%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o
+[ 71%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o
+[ 71%] 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/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
+[ 71%] 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/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
+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
+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
+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/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
+  232 |     out    << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__;
+      |                                                                ^~~~~~~~
+[ 71%] Built target utils
+make  -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend
+make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.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'
+[ 72%] 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
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
+[ 73%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
+/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
+      |                                                     ^~~~~~~~
+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
+[ 74%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
+[ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o
+[ 75%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o
+[ 75%] 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/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.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/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
+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
+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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
+[ 75%] 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/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
+[ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o
+[ 77%] 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/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
+[ 78%] 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/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
+[ 78%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o
+[ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o
+[ 78%] 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/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
+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
+[ 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/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
+[ 79%] 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/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
+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
+[ 79%] 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/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
+[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o
+[ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o
+[ 81%] 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/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp
+[ 81%] Building CXX object model/CMakeFiles/model.dir/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/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
+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
+[ 81%] 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/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
+[ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o
+[ 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/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
+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
+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
+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
+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
+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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:27:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/alignment/alignment.h:15:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 64%] Building CXX object 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
-[ 64%] 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
-[ 65%] 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
-[ 65%] 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
-[ 66%] 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/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/timetree.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8764,45 +9091,38 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 66%] Building CXX object pda/CMakeFiles/pda.dir/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
-[ 66%] 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
-[ 67%] 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/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/main.cpp:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitset.h:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.cpp:22:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/bits/refwrap.h:39,
                  from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:25:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8812,63 +9132,41 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 67%] Building CXX object pda/CMakeFiles/pda.dir/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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/split.h:27,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:26,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/splitgraph.h:24:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.h:12,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/pda/ecopd.cpp:8:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 68%] 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
 In 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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
 In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/fstream:40,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:52:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratekategory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8881,9 +9179,10 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8893,85 +9192,13 @@
 /usr/include/c++/14/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"
-/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) {
-      |                                                                                            ^~~~~
-/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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:21,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp:12:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/ostream:40,
-                 from /usr/include/c++/14/iostream:41,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/phylo-yaml/statespace.h:17:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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'
-[ 69%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 70%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o
-[ 70%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o
-[ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-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
-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
-[ 71%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 71%] 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/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
-[ 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/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
-[ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o
-[ 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/partitionmodelplen.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/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.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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -8985,9 +9212,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategamma.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9017,8 +9242,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratefree.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9032,9 +9256,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9049,8 +9271,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9065,7 +9287,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rategammainvar.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9075,35 +9298,13 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:16,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.cpp:12:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelsubst.h:15:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9117,27 +9318,25 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 74%] Building CXX object 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/model/rategamma.cpp:22:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9151,114 +9350,25 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.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*) {
-      |                                      ^~~~~
-[ 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
-/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) {
-      |                                           ^~~~~
-[ 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/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);
-      |                                             ^~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9268,39 +9378,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12:
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23:
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  146 |         virtual void readRates(istream &in) throw(const char*, string);
-      |                                             ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  153 |         virtual void readRates(string str) throw(const char*);
-      |                                            ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  160 |         virtual void readStateFreq(istream &in) throw(const char*);
-      |                                                 ^~~~~
-/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
-  167 |         virtual void readStateFreq(string str) throw(const char*);
-      |                                                ^~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9310,17 +9393,11 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 75%] Linking CXX static library libpda.a
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1
-[ 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
-/usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9334,7 +9411,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9344,29 +9421,12 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 76%] Building CXX object model/CMakeFiles/model.dir/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
-/usr/bin/ranlib libpda.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 76%] Built target pda
-make  -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend
-[ 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
-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
-/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/ratefree.cpp:8:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9380,9 +9440,11 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9392,13 +9454,12 @@
 /usr/include/c++/14/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.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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/rateinvar.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactory.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9408,45 +9469,28 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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/main/main.cpp:37:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9460,27 +9504,26 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 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
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9490,26 +9533,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-[ 80%] Building CXX object model/CMakeFiles/model.dir/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
-[ 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*) {
-      |                                         ^~~~~
-[ 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
-/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*) {
-      |                                             ^~~~~
-[ 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
+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);
       |                                             ^~~~~
@@ -9522,45 +9546,12 @@
 /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/modelmixture.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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 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
-[ 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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9570,6 +9561,7 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37:
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -9582,69 +9574,15 @@
 /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/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
-  927 |             << iqtree_VERSION_PATCH << " built " << __DATE__ << endl
-      |                                                     ^~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/string:49,
-                 from /usr/include/c++/14/bits/locale_classes.h:40,
-                 from /usr/include/c++/14/bits/ios_base.h:41,
-                 from /usr/include/c++/14/ios:44,
-                 from /usr/include/c++/14/istream:40,
-                 from /usr/include/c++/14/sstream:40,
-                 from /usr/include/c++/14/complex:45,
-                 from /usr/include/eigen3/Eigen/Core:50,
-                 from /usr/include/eigen3/Eigen/Dense:1,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomo.h:4,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   91 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   69 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21:
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -9657,34 +9595,18 @@
 /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:
+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/model/modelmixture.cpp:10:
+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/model/modelmixture.cpp:13:
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34:
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
    78 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:8:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -9697,24 +9619,6 @@
 /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.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/main/phyloanalysis.cpp:27:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 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);
       |                                             ^~~~~
@@ -9727,50 +9631,41 @@
 /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/modelmarkov.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*);
       |                                            ^~~~~
+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: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:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  153 |         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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:15:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h: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.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) {
+      |                                              ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  146 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
   146 |         virtual void readRates(istream &in) throw(const char*, string);
       |                                             ^~~~~
@@ -9783,23 +9678,54 @@
 /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*);
+      |                                                ^~~~~
+/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/modelmarkov.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/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:44,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/main/treetesting.cpp:15:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/utils/tools.h:27:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
+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);
       |                                             ^~~~~
@@ -9812,7 +9738,16 @@
 /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/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/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  892 | void ModelProtein::readRates(istream &in) throw(const char*, string) {
+      |                                           ^~~~~
+/build/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);
       |                                             ^~~~~
@@ -9825,18 +9760,109 @@
 /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:
+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/main/phylotesting.cpp:31:
+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/main/phylotesting.cpp:34:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  146 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  153 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  160 |         virtual void readStateFreq(istream &in) throw(const char*);
+      |                                                 ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  167 |         virtual void readStateFreq(string str) throw(const char*);
+      |                                                ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/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/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+   91 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  146 |         virtual void readRates(istream &in) throw(const char*, string);
+      |                                             ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  153 |         virtual void readRates(string str) throw(const char*);
+      |                                            ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  160 |         virtual void readStateFreq(istream &in) throw(const char*);
+      |                                                 ^~~~~
+/build/reproducible-path/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
+  167 |         virtual void readStateFreq(string str) throw(const char*);
+      |                                                ^~~~~
+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*);
+      |                                                ^~~~~
+/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/model/modelmarkov.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/string:49,
+                 from /usr/include/c++/14/bits/locale_classes.h:40,
+                 from /usr/include/c++/14/bits/ios_base.h:41,
+                 from /usr/include/c++/14/ios:44,
+                 from /usr/include/c++/14/istream:40,
+                 from /usr/include/c++/14/sstream:40,
+                 from /usr/include/c++/14/complex:45,
+                 from /usr/include/eigen3/Eigen/Core:50,
+                 from /usr/include/eigen3/Eigen/Dense:1,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:20:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 /build/reproducible-path/iqtree-2.0.7+dfsg/main/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 | }
@@ -9845,7 +9871,6 @@
 /build/reproducible-path/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type]
   257 | }
       | ^
-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);
       |                                             ^~~~~
@@ -9858,14 +9883,25 @@
 /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);
+/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*) {
       |                                             ^~~~~
+[ 83%] 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'
+[ 83%] Built target phyloYAML
 [ 84%] 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
@@ -9885,22 +9921,22 @@
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1
 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o
 /usr/bin/ranlib libalignment.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 85%] Built target alignment
-[ 85%] Linking CXX static library libkernelavx.a
-/usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake
-/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1
-/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
-/usr/bin/ranlib libkernelavx.a
-make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 85%] Built target kernelavx
 [ 86%] Linking CXX static library libkernelfma.a
 /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake
 /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1
 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o
 /usr/bin/ranlib libkernelfma.a
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
 [ 86%] Built target kernelfma
+[ 86%] Built target alignment
+[ 86%] Linking CXX static library libkernelavx.a
+/usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake
+/usr/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1
+/usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o
+/usr/bin/ranlib libkernelavx.a
+make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
+[ 86%] Built target kernelavx
 [ 87%] Linking CXX static library libmodel.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1
@@ -9914,49 +9950,59 @@
 make[4]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
 make  -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build
 make[4]: Entering directory '/build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi'
-[ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
-[ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
-[ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.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/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/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/mtree.cpp.o
+[ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o
+[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o
 [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o
-[ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o
-[ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.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/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp
-[ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/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.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/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.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/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/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.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/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.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/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/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
+[ 91%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o
+[ 91%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o
+[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o
+[ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o
+[ 92%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o
 [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o
+[ 92%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
+[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
+[ 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/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.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/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp
+cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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/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
+[ 95%] 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/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.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/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.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/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
+[ 95%] 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/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
+[ 95%] 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/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
+[ 96%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o
+[ 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/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp
-[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o
-[ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o
-cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 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/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
+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
+[ 97%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -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
-[ 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/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
 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
+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
+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
+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
+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/node.cpp:22:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/ncbitree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9968,9 +10014,8 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9982,9 +10027,7 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -9998,14 +10041,14 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
@@ -10013,6 +10056,14 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/quartet.cpp:12:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp:10:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
@@ -10023,10 +10074,17 @@
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.cpp:12:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mexttree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10039,8 +10097,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.h:24,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/matree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10052,9 +10110,9 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/supernode.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10066,9 +10124,9 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/constrainttree.cpp:11:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10083,8 +10141,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.h:17,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10097,7 +10155,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h: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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10128,7 +10187,39 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp:20:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10157,8 +10248,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/candidateset.cpp:9:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10170,9 +10260,22 @@
       |            ^~~~~~~~~~~~~~~
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonode.h:15,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.h:13,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp:9:
+/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
+  172 |   : public binary_function<NxsString, NxsString, bool>
+      |            ^~~~~~~~~~~~~~~
+In file included from /usr/include/c++/14/bits/refwrap.h:39,
+                 from /usr/include/c++/14/vector:68,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
+  131 |     struct binary_function
+      |            ^~~~~~~~~~~~~~~
+In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/memslot.cpp:22:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10187,7 +10290,8 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/discordance.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10200,8 +10304,8 @@
 In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtreeset.cpp:20:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10216,9 +10320,7 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:22:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
@@ -10232,17 +10334,21 @@
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
                  from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.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:
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertree.h:23,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.h:11,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp:8:
 /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
   172 |   : public binary_function<NxsString, NxsString, bool>
       |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
+In file included from /usr/include/c++/14/bits/stl_tree.h:65,
+                 from /usr/include/c++/14/set:62,
+                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
   131 |     struct binary_function
       |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35:
+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);
       |                                             ^~~~~
@@ -10255,25 +10361,21 @@
 /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
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29:
+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*);
       |                                            ^~~~~
-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
 /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/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
 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:
+                 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);
       |                                             ^~~~~
@@ -10286,10 +10388,7 @@
 /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.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:
+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);
       |                                             ^~~~~
@@ -10302,53 +10401,6 @@
 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-[ 97%] Building CXX object tree/CMakeFiles/tree.dir/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/tinatree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/tinatree.cpp:20:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/refwrap.h:39,
-                 from /usr/include/c++/14/vector:68,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
-In file included from /build/reproducible-path/iqtree-2.0.7+dfsg/ncl/ncl.h:91,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/node.h:37,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/mtree.h:23,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/phylotree.h:36,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:29,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.h:11,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/parstree.cpp:9:
-/build/reproducible-path/iqtree-2.0.7+dfsg/ncl/nxsstring.h:172:12: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 /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 | }
@@ -10357,22 +10409,6 @@
 /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<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
-  172 |   : public binary_function<NxsString, NxsString, bool>
-      |            ^~~~~~~~~~~~~~~
-In file included from /usr/include/c++/14/bits/stl_tree.h:65,
-                 from /usr/include/c++/14/set:62,
-                 from /build/reproducible-path/iqtree-2.0.7+dfsg/tree/iqtree.h:25:
-/usr/include/c++/14/bits/stl_function.h:131:12: note: declared here
-  131 |     struct binary_function
-      |            ^~~~~~~~~~~~~~~
 [ 98%] Linking CXX static library libtree.a
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake
 cd /build/reproducible-path/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1
@@ -10451,215 +10487,188 @@
 echo 'time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo' >> example.short
 time sh example.short
 Executing tests using /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp ...
-+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy
++ /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:    ionos1-amd64 (AVX, 78 GB RAM)
+Host:    i-capture-the-hostname (AVX2, FMA3, 78 GB RAM)
 Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy
-Seed:    673059 (Using SPRNG - Scalable Parallel Random Number Generator)
-Time:    Tue Nov  5 18:02:49 2024
-Kernel:  AVX - 1 threads (20 CPU cores detected)
+Seed:    891659 (Using SPRNG - Scalable Parallel Random Number Generator)
+Time:    Mon Dec  8 23:52:35 2025
+Kernel:  AVX+FMA - 1 threads (42 CPU cores detected)
 
-HINT: Use -nt option to specify number of threads because your CPU has 20 cores!
+HINT: Use -nt option to specify number of threads because your CPU has 42 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)
+Alignment has 17 sequences with 1998 columns, 1152 distinct patterns
+1009 parsimony-informative, 303 singleton sites, 686 constant sites
+           Gap/Ambiguity  Composition  p-value
+   1  LngfishAu    0.15%    passed      6.20%
+   2  LngfishSA    0.00%    failed      0.62%
+   3  LngfishAf    0.05%    failed      1.60%
+   4  Frog         0.05%    passed     58.01%
+   5  Turtle       0.15%    passed     44.25%
+   6  Sphenodon    0.10%    passed     59.78%
+   7  Lizard       0.90%    passed     38.67%
+   8  Crocodile    0.35%    failed      2.51%
+   9  Bird         0.00%    failed      0.00%
+  10  Human        0.00%    failed      0.85%
+  11  Seal         0.00%    passed     68.93%
+  12  Cow          0.00%    passed     59.11%
+  13  Whale        0.00%    passed     97.83%
+  14  Mouse        0.05%    failed      1.43%
+  15  Rat          0.00%    passed     39.69%
+  16  Platypus     0.00%    failed      3.46%
+  17  Opossum      0.00%    failed      0.01%
+****  TOTAL        0.11%  8 sequences failed composition chi2 test (p-value<5%; df=3)
 
 
-Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.022 seconds
+Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 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: -11227.707
-Optimal log-likelihood: -11227.579
-Rate parameters:  A-C: 1.43562  A-G: 2.28898  A-T: 1.71639  C-G: 1.87008  C-T: 2.77863  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: 1.510
-Parameters optimization took 1 rounds (0.528 sec)
-Time for fast ML tree search: 3.324 seconds
+1. Initial log-likelihood: -21149.239
+Optimal log-likelihood: -21149.100
+Rate parameters:  A-C: 3.73650  A-G: 5.18609  A-T: 3.83480  C-G: 0.41900  C-T: 15.29543  G-T: 1.00000
+Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
+Proportion of invariable sites: 0.157
+Gamma shape alpha: 0.739
+Parameters optimization took 1 rounds (0.035 sec)
+Time for fast ML tree search: 0.396 seconds
 
-NOTE: ModelFinder requires 5 MB RAM!
-ModelFinder will test up to 286 DNA models (sample size: 384) ...
+NOTE: ModelFinder requires 6 MB RAM!
+ModelFinder will test up to 286 DNA models (sample size: 1998) ...
  No. Model         -LnL         df  AIC          AICc         BIC
-  1  GTR+F         11794.990    93  23775.980    23836.269    24143.389
-  2  GTR+F+I       11552.136    94  23292.271    23354.071    23663.632
-  3  GTR+F+G4      11242.957    94  22673.915    22735.714    23045.275
-  4  GTR+F+I+G4    11227.585    95  22645.169    22708.503    23020.480
-  5  GTR+F+R2      11339.372    95  22868.743    22932.077    23244.054
-  6  GTR+F+R3      11228.752    97  22651.505    22717.980    23034.717
-  7  GTR+F+R4      11221.371    99  22640.742    22710.460    23031.855
-  8  GTR+F+R5      11221.263    101 22644.527    22717.590    23043.542
- 17  SYM+I+G4      11230.670    92  22645.340    22704.144    23008.799
- 30  TVM+F+I+G4    11230.335    94  22648.670    22710.470    23020.031
- 43  TVMe+I+G4     11232.752    91  22647.505    22704.847    23007.013
- 56  TIM3+F+I+G4   11240.764    93  22667.529    22727.819    23034.939
- 69  TIM3e+I+G4    11244.479    90  22668.958    22724.863    23024.516
- 82  TIM2+F+I+G4   11243.919    93  22673.838    22734.128    23041.248
- 95  TIM2e+I+G4    11251.354    90  22682.708    22738.612    23038.266
-108  TIM+F+I+G4    11232.389    93  22650.778    22711.067    23018.187
-121  TIMe+I+G4     11238.984    90  22657.969    22713.873    23013.527
-134  TPM3u+F+I+G4  11243.660    92  22671.319    22730.124    23034.779
-147  TPM3+F+I+G4   11243.660    92  22671.319    22730.124    23034.779
-160  TPM2u+F+I+G4  11246.725    92  22677.451    22736.255    23040.910
-173  TPM2+F+I+G4   11246.725    92  22677.451    22736.255    23040.910
-186  K3Pu+F+I+G4   11235.105    92  22654.210    22713.014    23017.669
-199  K3P+I+G4      11240.922    89  22659.844    22714.334    23011.451
-212  TN+F+I+G4     11244.046    92  22672.092    22730.896    23035.551
-225  TNe+I+G4      11251.403    89  22680.806    22735.296    23032.413
-238  HKY+F+I+G4    11246.875    91  22675.751    22733.093    23035.259
-251  K2P+I+G4      11253.426    88  22682.852    22735.950    23030.509
-264  F81+F+I+G4    11295.600    90  22771.199    22827.104    23126.757
-277  JC+I+G4       11299.439    87  22772.877    22824.607    23116.583
-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
+  1  GTR+F         22701.500    39  45481.000    45482.593    45699.396
+  2  GTR+F+I       21615.547    40  43311.094    43312.770    43535.090
+  3  GTR+F+G4      21155.970    40  42391.940    42393.616    42615.936
+  4  GTR+F+I+G4    21148.849    41  42379.699    42381.459    42609.295
+  5  GTR+F+R2      21235.663    41  42553.327    42555.087    42782.923
+  6  GTR+F+R3      21147.168    43  42380.337    42382.273    42621.132
+  7  GTR+F+R4      21145.837    45  42381.675    42383.796    42633.671
+ 16  SYM+G4        21317.782    37  42709.563    42710.998    42916.760
+ 17  SYM+I+G4      21306.170    38  42688.341    42689.854    42901.137
+ 29  TVM+F+G4      21300.237    39  42678.474    42680.067    42896.870
+ 30  TVM+F+I+G4    21288.270    40  42656.541    42658.217    42880.537
+ 42  TVMe+G4       21422.186    36  42916.372    42917.730    43117.968
+ 43  TVMe+I+G4     21407.596    37  42889.191    42890.626    43096.388
+ 55  TIM3+F+G4     21367.926    38  42811.853    42813.366    43024.649
+ 56  TIM3+F+I+G4   21359.476    39  42796.953    42798.546    43015.349
+ 68  TIM3e+G4      21717.462    35  43504.924    43506.209    43700.921
+ 69  TIM3e+I+G4    21708.558    36  43489.115    43490.473    43690.711
+ 81  TIM2+F+G4     21159.708    38  42395.415    42396.928    42608.212
+ 82  TIM2+F+I+G4   21152.489    39  42382.979    42384.572    42601.375
+ 94  TIM2e+G4      21320.880    35  42711.760    42713.045    42907.757
+ 95  TIM2e+I+G4    21309.127    36  42690.254    42691.613    42891.851
+107  TIM+F+G4      21368.780    38  42813.560    42815.073    43026.356
+108  TIM+F+I+G4    21360.237    39  42798.474    42800.068    43016.871
+120  TIMe+G4       21718.131    35  43506.262    43507.546    43702.258
+121  TIMe+I+G4     21709.220    36  43490.439    43491.798    43692.036
+133  TPM3u+F+G4    21488.892    37  43051.785    43053.219    43258.981
+134  TPM3u+F+I+G4  21474.934    38  43025.868    43027.381    43238.664
+146  TPM3+F+G4     21488.892    37  43051.785    43053.219    43258.981
+147  TPM3+F+I+G4   21474.934    38  43025.868    43027.381    43238.664
+159  TPM2u+F+G4    21303.797    37  42681.594    42683.029    42888.790
+160  TPM2u+F+I+G4  21291.866    38  42659.732    42661.245    42872.529
+172  TPM2+F+G4     21303.797    37  42681.594    42683.029    42888.790
+173  TPM2+F+I+G4   21291.866    38  42659.732    42661.245    42872.529
+185  K3Pu+F+G4     21489.348    37  43052.695    43054.130    43259.892
+186  K3Pu+F+I+G4   21475.443    38  43026.886    43028.399    43239.682
+198  K3P+G4        21847.491    34  43762.981    43764.193    43953.378
+199  K3P+I+G4      21833.794    35  43737.589    43738.873    43933.586
+211  TN+F+G4       21369.048    37  42812.095    42813.530    43019.292
+212  TN+F+I+G4     21360.511    38  42797.021    42798.534    43009.817
+224  TNe+G4        21718.201    34  43504.403    43505.615    43694.799
+225  TNe+I+G4      21709.280    35  43488.559    43489.844    43684.556
+237  HKY+F+G4      21489.737    36  43051.474    43052.832    43253.070
+238  HKY+F+I+G4    21475.767    37  43025.533    43026.968    43232.730
+250  K2P+G4        21847.675    33  43761.350    43762.492    43946.146
+251  K2P+I+G4      21833.947    34  43735.895    43737.107    43926.292
+263  F81+F+G4      22031.578    35  44133.155    44134.440    44329.152
+264  F81+F+I+G4    22019.574    36  44111.147    44112.506    44312.744
+276  JC+G4         22258.086    32  44580.172    44581.246    44759.368
+277  JC+I+G4       22245.552    33  44557.104    44558.247    44741.901
+Akaike Information Criterion:           GTR+F+I+G4
+Corrected Akaike Information Criterion: GTR+F+I+G4
+Bayesian Information Criterion:         TIM2+F+I+G4
+Best-fit model: TIM2+F+I+G4 chosen according to BIC
 
 All model information printed to example.phy.model.gz
-CPU time for ModelFinder: 9.875 seconds (0h:0m:9s)
-Wall-clock time for ModelFinder: 23.840 seconds (0h:0m:23s)
+CPU time for ModelFinder: 5.908 seconds (0h:0m:5s)
+Wall-clock time for ModelFinder: 5.945 seconds (0h:0m:5s)
 
 NOTE: 2 MB RAM (0 GB) is required!
 Estimate model parameters (epsilon = 0.100)
 Thoroughly optimizing +I+G parameters from 10 start values...
-Init pinv, alpha: 0.000, 1.556 / Estimate: 0.000, 0.953 / LogL: -11247.148
-Init pinv, alpha: 0.012, 1.556 / Estimate: 0.084, 1.548 / LogL: -11232.748
-Init pinv, alpha: 0.023, 1.556 / Estimate: 0.083, 1.545 / LogL: -11232.750
-Init pinv, alpha: 0.035, 1.556 / Estimate: 0.083, 1.545 / LogL: -11232.752
-Init pinv, alpha: 0.046, 1.556 / Estimate: 0.084, 1.547 / LogL: -11232.750
-Init pinv, alpha: 0.058, 1.556 / Estimate: 0.083, 1.544 / LogL: -11232.755
-Init pinv, alpha: 0.069, 1.556 / Estimate: 0.083, 1.541 / LogL: -11232.758
-Init pinv, alpha: 0.081, 1.556 / Estimate: 0.083, 1.547 / LogL: -11232.752
-Init pinv, alpha: 0.093, 1.556 / Estimate: 0.085, 1.559 / LogL: -11232.751
-Init pinv, alpha: 0.104, 1.556 / Estimate: 0.085, 1.565 / LogL: -11232.759
-Optimal pinv,alpha: 0.084, 1.548 / LogL: -11232.748
+Init pinv, alpha: 0.000, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748
+Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.976
+Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.640
+Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.216
+Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.516
+Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778
+Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833
+Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.812 / LogL: -21152.858
+Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876
+Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.904
+Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.516
 
-Parameters optimization took 8.820 sec
-Computing ML distances based on estimated model parameters... 0.061 sec
+Parameters optimization took 1.480 sec
+Computing ML distances based on estimated model parameters... 0.006 sec
 Computing BIONJ tree...
-0.002 seconds
-Log-likelihood of BIONJ tree: -11270.862
+0.000 seconds
+Log-likelihood of BIONJ tree: -21157.740
 --------------------------------------------------------------------
 |             INITIALIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Generating 98 parsimony trees... 2.849 second
-Computing log-likelihood of 98 initial trees ... 7.446 seconds
-Current best score: -11232.748
+Generating 98 parsimony trees... 0.232 second
+Computing log-likelihood of 98 initial trees ... 0.473 seconds
+Current best score: -21152.516
 
 Do NNI search on 20 best initial trees
 Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 1: -11231.664
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 2: -11224.924
-Iteration 10 / LogL: -11226.741 / Time: 0h:0m:29s
-Iteration 20 / LogL: -11233.034 / Time: 0h:0m:40s
-Finish initializing candidate tree set (16)
-Current best tree score: -11224.924 / CPU time: 31.319
+BETTER TREE FOUND at iteration 1: -21152.511
+Iteration 10 / LogL: -21158.159 / Time: 0h:0m:2s
+Iteration 20 / LogL: -21152.517 / Time: 0h:0m:3s
+Finish initializing candidate tree set (2)
+Current best tree score: -21152.511 / CPU time: 1.800
 Number of iterations: 20
 --------------------------------------------------------------------
 |               OPTIMIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 24: -11224.088
-Iteration 30 / LogL: -11224.660 / Time: 0h:0m:54s (0h:2m:58s left)
-UPDATE BEST LOG-LIKELIHOOD: -11224.082
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 37: -11223.620
-Iteration 40 / LogL: -11224.221 / Time: 0h:1m:10s (0h:2m:55s left)
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 46: -11223.520
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 48: -11223.411
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 50: -11223.037
-Iteration 50 / LogL: -11223.037 / Time: 0h:1m:24s (0h:2m:52s left)
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 55: -11222.773
-Iteration 60 / LogL: -11225.928 / Time: 0h:1m:39s (0h:2m:40s left)
-Iteration 70 / LogL: -11223.047 / Time: 0h:1m:55s (0h:2m:21s left)
-Iteration 80 / LogL: -11222.966 / Time: 0h:2m:8s (0h:2m:2s left)
-Iteration 90 / LogL: -11223.397 / Time: 0h:2m:24s (0h:1m:45s left)
-Iteration 100 / LogL: -11222.845 / Time: 0h:2m:38s (0h:1m:28s left)
-Iteration 110 / LogL: -11222.777 / Time: 0h:2m:54s (0h:1m:12s left)
-Iteration 120 / LogL: -11222.789 / Time: 0h:3m:8s (0h:0m:55s left)
-Iteration 130 / LogL: -11222.933 / Time: 0h:3m:21s (0h:0m:39s left)
-Iteration 140 / LogL: -11224.157 / Time: 0h:3m:39s (0h:0m:23s left)
-Iteration 150 / LogL: -11223.123 / Time: 0h:4m:0s (0h:0m:8s left)
-TREE SEARCH COMPLETED AFTER 156 ITERATIONS / Time: 0h:4m:13s
+Iteration 30 / LogL: -21152.683 / Time: 0h:0m:4s (0h:0m:9s left)
+Iteration 40 / LogL: -21154.336 / Time: 0h:0m:4s (0h:0m:7s left)
+Iteration 50 / LogL: -21152.751 / Time: 0h:0m:5s (0h:0m:5s left)
+Iteration 60 / LogL: -21153.180 / Time: 0h:0m:6s (0h:0m:4s left)
+Iteration 70 / LogL: -21152.518 / Time: 0h:0m:6s (0h:0m:3s left)
+Iteration 80 / LogL: -21152.525 / Time: 0h:0m:7s (0h:0m:2s left)
+Iteration 90 / LogL: -21153.029 / Time: 0h:0m:8s (0h:0m:1s left)
+Iteration 100 / LogL: -21152.553 / Time: 0h:0m:8s (0h:0m:0s left)
+TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:9s
 
 --------------------------------------------------------------------
 |                    FINALIZING TREE SEARCH                        |
 --------------------------------------------------------------------
 Performs final model parameters optimization
 Estimate model parameters (epsilon = 0.010)
-1. Initial log-likelihood: -11222.773
-Optimal log-likelihood: -11222.772
-Rate parameters:  A-C: 1.52407  A-G: 2.62269  A-T: 1.68230  C-G: 1.99201  C-T: 2.62269  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: 1.529
-Parameters optimization took 1 rounds (0.294 sec)
-BEST SCORE FOUND : -11222.772
-Total tree length: 12.602
-
-Total number of iterations: 156
-CPU time used for tree search: 89.679 sec (0h:1m:29s)
-Wall-clock time used for tree search: 243.900 sec (0h:4m:3s)
-Total CPU time used: 93.758 sec (0h:1m:33s)
-Total wall-clock time used: 253.482 sec (0h:4m:13s)
+1. Initial log-likelihood: -21152.511
+Optimal log-likelihood: -21152.507
+Rate parameters:  A-C: 5.70686  A-G: 7.79923  A-T: 5.70686  C-G: 1.00000  C-T: 23.13277  G-T: 1.00000
+Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
+Proportion of invariable sites: 0.154
+Gamma shape alpha: 0.728
+Parameters optimization took 1 rounds (0.018 sec)
+BEST SCORE FOUND : -21152.507
+Total tree length: 4.225
+
+Total number of iterations: 102
+CPU time used for tree search: 7.411 sec (0h:0m:7s)
+Wall-clock time used for tree search: 7.520 sec (0h:0m:7s)
+Total CPU time used: 8.938 sec (0h:0m:8s)
+Total wall-clock time used: 9.051 sec (0h:0m:9s)
 
 Analysis results written to: 
   IQ-TREE report:                example.phy.iqtree
@@ -10667,219 +10676,193 @@
   Likelihood distances:          example.phy.mldist
   Screen log file:               example.phy.log
 
-Date and Time: Tue Nov  5 18:07:27 2024
-103.63user 1.31system 4:37.55elapsed 37%CPU (0avgtext+0avgdata 14392maxresident)k
-7432inputs+544outputs (56major+5435minor)pagefaults 0swaps
-+ time /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo
+Date and Time: Mon Dec  8 23:52:50 2025
+
+real	0m15.007s
+user	0m14.857s
+sys	0m0.148s
++ /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:    ionos1-amd64 (AVX, 78 GB RAM)
+Host:    i-capture-the-hostname (AVX2, FMA3, 78 GB RAM)
 Command: /build/reproducible-path/iqtree-2.0.7+dfsg/build.omp/iqtree2-omp -s example.phy -redo
-Seed:    147454 (Using SPRNG - Scalable Parallel Random Number Generator)
-Time:    Tue Nov  5 18:07:27 2024
-Kernel:  AVX - 1 threads (20 CPU cores detected)
+Seed:    899315 (Using SPRNG - Scalable Parallel Random Number Generator)
+Time:    Mon Dec  8 23:52:50 2025
+Kernel:  AVX+FMA - 1 threads (42 CPU cores detected)
 
-HINT: Use -nt option to specify number of threads because your CPU has 20 cores!
+HINT: Use -nt option to specify number of threads because your CPU has 42 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)
+Alignment has 17 sequences with 1998 columns, 1152 distinct patterns
+1009 parsimony-informative, 303 singleton sites, 686 constant sites
+           Gap/Ambiguity  Composition  p-value
+   1  LngfishAu    0.15%    passed      6.20%
+   2  LngfishSA    0.00%    failed      0.62%
+   3  LngfishAf    0.05%    failed      1.60%
+   4  Frog         0.05%    passed     58.01%
+   5  Turtle       0.15%    passed     44.25%
+   6  Sphenodon    0.10%    passed     59.78%
+   7  Lizard       0.90%    passed     38.67%
+   8  Crocodile    0.35%    failed      2.51%
+   9  Bird         0.00%    failed      0.00%
+  10  Human        0.00%    failed      0.85%
+  11  Seal         0.00%    passed     68.93%
+  12  Cow          0.00%    passed     59.11%
+  13  Whale        0.00%    passed     97.83%
+  14  Mouse        0.05%    failed      1.43%
+  15  Rat          0.00%    passed     39.69%
+  16  Platypus     0.00%    failed      3.46%
+  17  Opossum      0.00%    failed      0.01%
+****  TOTAL        0.11%  8 sequences failed composition chi2 test (p-value<5%; df=3)
 
 
-Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.281 seconds
+Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 seconds
 Perform fast likelihood tree search using GTR+I+G model...
 Estimate model parameters (epsilon = 5.000)
 Perform nearest neighbor interchange...
 Estimate model parameters (epsilon = 1.000)
-1. Initial log-likelihood: -11222.570
-Optimal log-likelihood: -11222.453
-Rate parameters:  A-C: 1.48105  A-G: 2.35929  A-T: 1.79126  C-G: 1.92551  C-T: 2.87198  G-T: 1.00000
-Base frequencies:  A: 0.249  C: 0.262  G: 0.251  T: 0.239
-Proportion of invariable sites: 0.085
-Gamma shape alpha: 1.531
-Parameters optimization took 1 rounds (0.447 sec)
-Time for fast ML tree search: 3.886 seconds
+1. Initial log-likelihood: -21149.239
+Optimal log-likelihood: -21149.100
+Rate parameters:  A-C: 3.73650  A-G: 5.18609  A-T: 3.83480  C-G: 0.41900  C-T: 15.29543  G-T: 1.00000
+Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
+Proportion of invariable sites: 0.157
+Gamma shape alpha: 0.739
+Parameters optimization took 1 rounds (0.036 sec)
+Time for fast ML tree search: 0.369 seconds
 
-NOTE: ModelFinder requires 5 MB RAM!
-ModelFinder will test up to 286 DNA models (sample size: 384) ...
+NOTE: ModelFinder requires 6 MB RAM!
+ModelFinder will test up to 286 DNA models (sample size: 1998) ...
  No. Model         -LnL         df  AIC          AICc         BIC
-  1  GTR+F         11784.857    93  23755.713    23816.003    24123.123
-  2  GTR+F+I       11542.762    94  23273.525    23335.324    23644.885
-  3  GTR+F+G4      11238.119    94  22664.239    22726.038    23035.599
-  4  GTR+F+I+G4    11222.454    95  22634.908    22698.241    23010.219
-  5  GTR+F+R2      11332.079    95  22854.159    22917.492    23229.470
-  6  GTR+F+R3      11222.873    97  22639.746    22706.222    23022.959
-  7  GTR+F+R4      11216.534    99  22631.068    22700.786    23022.181
-  8  GTR+F+R5      11216.213    101 22634.426    22707.490    23033.441
- 17  SYM+I+G4      11225.586    92  22635.171    22693.976    22998.631
- 30  TVM+F+I+G4    11225.427    94  22638.855    22700.654    23010.215
- 43  TVMe+I+G4     11227.874    91  22637.749    22695.091    22997.257
- 56  TIM3+F+I+G4   11237.296    93  22660.591    22720.881    23028.001
- 69  TIM3e+I+G4    11240.994    90  22661.988    22717.893    23017.546
- 82  TIM2+F+I+G4   11240.873    93  22667.747    22728.037    23035.157
- 95  TIM2e+I+G4    11248.653    90  22677.305    22733.210    23032.863
-108  TIM+F+I+G4    11228.664    93  22643.327    22703.617    23010.737
-121  TIMe+I+G4     11235.522    90  22651.043    22706.948    23006.601
-134  TPM3u+F+I+G4  11240.439    92  22664.878    22723.682    23028.337
-147  TPM3+F+I+G4   11240.439    92  22664.878    22723.682    23028.337
-160  TPM2u+F+I+G4  11243.911    92  22671.821    22730.625    23035.280
-173  TPM2+F+I+G4   11243.911    92  22671.821    22730.625    23035.280
-186  K3Pu+F+I+G4   11231.608    92  22647.215    22706.019    23010.674
-199  K3P+I+G4      11237.658    89  22653.317    22707.806    23004.924
-212  TN+F+I+G4     11241.228    92  22666.457    22725.261    23029.916
-225  TNe+I+G4      11248.858    89  22675.716    22730.205    23027.323
-238  HKY+F+I+G4    11244.294    91  22670.587    22727.930    23030.096
-251  K2P+I+G4      11251.083    88  22678.166    22731.264    23025.823
-264  F81+F+I+G4    11294.363    90  22768.726    22824.630    23124.283
-277  JC+I+G4       11298.377    87  22770.754    22822.484    23114.460
-Akaike Information Criterion:           GTR+F+R4
-Corrected Akaike Information Criterion: SYM+I+G4
-Bayesian Information Criterion:         TVMe+I+G4
-Best-fit model: TVMe+I+G4 chosen according to BIC
+  1  GTR+F         22701.500    39  45481.000    45482.593    45699.396
+  2  GTR+F+I       21615.547    40  43311.094    43312.770    43535.090
+  3  GTR+F+G4      21155.970    40  42391.940    42393.616    42615.936
+  4  GTR+F+I+G4    21148.849    41  42379.699    42381.459    42609.295
+  5  GTR+F+R2      21235.663    41  42553.327    42555.087    42782.923
+  6  GTR+F+R3      21147.168    43  42380.337    42382.273    42621.132
+  7  GTR+F+R4      21145.837    45  42381.675    42383.796    42633.671
+ 16  SYM+G4        21317.782    37  42709.563    42710.998    42916.760
+ 17  SYM+I+G4      21306.170    38  42688.341    42689.854    42901.137
+ 29  TVM+F+G4      21300.237    39  42678.474    42680.067    42896.870
+ 30  TVM+F+I+G4    21288.270    40  42656.541    42658.217    42880.537
+ 42  TVMe+G4       21422.186    36  42916.372    42917.730    43117.968
+ 43  TVMe+I+G4     21407.596    37  42889.191    42890.626    43096.388
+ 55  TIM3+F+G4     21367.926    38  42811.853    42813.366    43024.649
+ 56  TIM3+F+I+G4   21359.476    39  42796.953    42798.546    43015.349
+ 68  TIM3e+G4      21717.462    35  43504.924    43506.209    43700.921
+ 69  TIM3e+I+G4    21708.558    36  43489.115    43490.473    43690.711
+ 81  TIM2+F+G4     21159.708    38  42395.415    42396.928    42608.212
+ 82  TIM2+F+I+G4   21152.489    39  42382.979    42384.572    42601.375
+ 94  TIM2e+G4      21320.880    35  42711.760    42713.045    42907.757
+ 95  TIM2e+I+G4    21309.127    36  42690.254    42691.613    42891.851
+107  TIM+F+G4      21368.780    38  42813.560    42815.073    43026.356
+108  TIM+F+I+G4    21360.237    39  42798.474    42800.068    43016.871
+120  TIMe+G4       21718.131    35  43506.262    43507.546    43702.258
+121  TIMe+I+G4     21709.220    36  43490.439    43491.798    43692.036
+133  TPM3u+F+G4    21488.892    37  43051.785    43053.219    43258.981
+134  TPM3u+F+I+G4  21474.934    38  43025.868    43027.381    43238.664
+146  TPM3+F+G4     21488.892    37  43051.785    43053.219    43258.981
+147  TPM3+F+I+G4   21474.934    38  43025.868    43027.381    43238.664
+159  TPM2u+F+G4    21303.797    37  42681.594    42683.029    42888.790
+160  TPM2u+F+I+G4  21291.866    38  42659.732    42661.245    42872.529
+172  TPM2+F+G4     21303.797    37  42681.594    42683.029    42888.790
+173  TPM2+F+I+G4   21291.866    38  42659.732    42661.245    42872.529
+185  K3Pu+F+G4     21489.348    37  43052.695    43054.130    43259.892
+186  K3Pu+F+I+G4   21475.443    38  43026.886    43028.399    43239.682
+198  K3P+G4        21847.491    34  43762.981    43764.193    43953.378
+199  K3P+I+G4      21833.794    35  43737.589    43738.873    43933.586
+211  TN+F+G4       21369.048    37  42812.095    42813.530    43019.292
+212  TN+F+I+G4     21360.511    38  42797.021    42798.534    43009.817
+224  TNe+G4        21718.201    34  43504.403    43505.615    43694.799
+225  TNe+I+G4      21709.280    35  43488.559    43489.844    43684.556
+237  HKY+F+G4      21489.737    36  43051.474    43052.832    43253.070
+238  HKY+F+I+G4    21475.767    37  43025.533    43026.968    43232.730
+250  K2P+G4        21847.675    33  43761.350    43762.492    43946.146
+251  K2P+I+G4      21833.947    34  43735.895    43737.107    43926.292
+263  F81+F+G4      22031.578    35  44133.155    44134.440    44329.152
+264  F81+F+I+G4    22019.574    36  44111.147    44112.506    44312.744
+276  JC+G4         22258.086    32  44580.172    44581.246    44759.368
+277  JC+I+G4       22245.552    33  44557.104    44558.247    44741.901
+Akaike Information Criterion:           GTR+F+I+G4
+Corrected Akaike Information Criterion: GTR+F+I+G4
+Bayesian Information Criterion:         TIM2+F+I+G4
+Best-fit model: TIM2+F+I+G4 chosen according to BIC
 
 All model information printed to example.phy.model.gz
-CPU time for ModelFinder: 9.368 seconds (0h:0m:9s)
-Wall-clock time for ModelFinder: 27.564 seconds (0h:0m:27s)
+CPU time for ModelFinder: 5.932 seconds (0h:0m:5s)
+Wall-clock time for ModelFinder: 5.996 seconds (0h:0m:5s)
 
 NOTE: 2 MB RAM (0 GB) is required!
 Estimate model parameters (epsilon = 0.100)
 Thoroughly optimizing +I+G parameters from 10 start values...
-Init pinv, alpha: 0.000, 1.576 / Estimate: 0.000, 0.961 / LogL: -11242.448
-Init pinv, alpha: 0.012, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.871
-Init pinv, alpha: 0.023, 1.576 / Estimate: 0.084, 1.565 / LogL: -11227.873
-Init pinv, alpha: 0.035, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.875
-Init pinv, alpha: 0.046, 1.576 / Estimate: 0.084, 1.568 / LogL: -11227.874
-Init pinv, alpha: 0.058, 1.576 / Estimate: 0.083, 1.564 / LogL: -11227.878
-Init pinv, alpha: 0.069, 1.576 / Estimate: 0.083, 1.562 / LogL: -11227.880
-Init pinv, alpha: 0.081, 1.576 / Estimate: 0.084, 1.567 / LogL: -11227.872
-Init pinv, alpha: 0.093, 1.576 / Estimate: 0.085, 1.579 / LogL: -11227.874
-Init pinv, alpha: 0.104, 1.576 / Estimate: 0.085, 1.585 / LogL: -11227.881
-Optimal pinv,alpha: 0.084, 1.568 / LogL: -11227.871
+Init pinv, alpha: 0.000, 0.738 / Estimate: 0.000, 0.483 / LogL: -21159.748
+Init pinv, alpha: 0.038, 0.738 / Estimate: 0.043, 0.532 / LogL: -21156.976
+Init pinv, alpha: 0.076, 0.738 / Estimate: 0.085, 0.592 / LogL: -21154.640
+Init pinv, alpha: 0.114, 0.738 / Estimate: 0.120, 0.654 / LogL: -21153.216
+Init pinv, alpha: 0.153, 0.738 / Estimate: 0.153, 0.726 / LogL: -21152.516
+Init pinv, alpha: 0.191, 0.738 / Estimate: 0.183, 0.803 / LogL: -21152.778
+Init pinv, alpha: 0.229, 0.738 / Estimate: 0.185, 0.810 / LogL: -21152.833
+Init pinv, alpha: 0.267, 0.738 / Estimate: 0.186, 0.812 / LogL: -21152.858
+Init pinv, alpha: 0.305, 0.738 / Estimate: 0.186, 0.813 / LogL: -21152.876
+Init pinv, alpha: 0.343, 0.738 / Estimate: 0.187, 0.816 / LogL: -21152.904
+Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.516
 
-Parameters optimization took 8.820 sec
-Computing ML distances based on estimated model parameters... 0.057 sec
+Parameters optimization took 1.478 sec
+Computing ML distances based on estimated model parameters... 0.006 sec
 Computing BIONJ tree...
-0.002 seconds
-Log-likelihood of BIONJ tree: -11270.850
+0.000 seconds
+Log-likelihood of BIONJ tree: -21157.740
 --------------------------------------------------------------------
 |             INITIALIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Generating 98 parsimony trees... 1.688 second
-Computing log-likelihood of 98 initial trees ... 5.322 seconds
-Current best score: -11227.871
+Generating 98 parsimony trees... 0.232 second
+Computing log-likelihood of 98 initial trees ... 0.470 seconds
+Current best score: -21152.516
 
 Do NNI search on 20 best initial trees
 Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 1: -11226.734
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 5: -11226.438
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 6: -11225.853
-Iteration 10 / LogL: -11227.686 / Time: 0h:0m:29s
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 13: -11225.467
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 20: -11224.869
-Iteration 20 / LogL: -11224.869 / Time: 0h:0m:44s
-Finish initializing candidate tree set (17)
-Current best tree score: -11224.869 / CPU time: 34.883
+BETTER TREE FOUND at iteration 1: -21152.511
+Iteration 10 / LogL: -21152.699 / Time: 0h:0m:2s
+Iteration 20 / LogL: -21152.713 / Time: 0h:0m:3s
+Finish initializing candidate tree set (2)
+Current best tree score: -21152.511 / CPU time: 1.855
 Number of iterations: 20
 --------------------------------------------------------------------
 |               OPTIMIZING CANDIDATE TREE SET                      |
 --------------------------------------------------------------------
-Iteration 30 / LogL: -11225.935 / Time: 0h:0m:57s (0h:2m:58s left)
-Iteration 40 / LogL: -11227.489 / Time: 0h:1m:10s (0h:2m:24s left)
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 46: -11223.409
-Iteration 50 / LogL: -11223.424 / Time: 0h:1m:27s (0h:2m:51s left)
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 57: -11223.144
-Estimate model parameters (epsilon = 0.100)
-BETTER TREE FOUND at iteration 59: -11222.775
-Iteration 60 / LogL: -11223.426 / Time: 0h:1m:42s (0h:2m:51s left)
-Iteration 70 / LogL: -11224.070 / Time: 0h:1m:57s (0h:2m:30s left)
-UPDATE BEST LOG-LIKELIHOOD: -11222.774
-Iteration 80 / LogL: -11222.774 / Time: 0h:2m:11s (0h:2m:11s left)
-Iteration 90 / LogL: -11222.811 / Time: 0h:2m:25s (0h:1m:52s left)
-Iteration 100 / LogL: -11226.529 / Time: 0h:2m:39s (0h:1m:34s left)
-Iteration 110 / LogL: -11222.791 / Time: 0h:2m:51s (0h:1m:17s left)
-Iteration 120 / LogL: -11222.798 / Time: 0h:3m:4s (0h:1m:0s left)
-Iteration 130 / LogL: -11223.056 / Time: 0h:3m:21s (0h:0m:45s left)
-Iteration 140 / LogL: -11222.991 / Time: 0h:3m:34s (0h:0m:29s left)
-Iteration 150 / LogL: -11223.223 / Time: 0h:3m:48s (0h:0m:13s left)
-Iteration 160 / LogL: -11224.478 / Time: 0h:4m:0s (0h:0m:-2s left)
-TREE SEARCH COMPLETED AFTER 160 ITERATIONS / Time: 0h:4m:0s
+Iteration 30 / LogL: -21152.852 / Time: 0h:0m:4s (0h:0m:9s left)
+Iteration 40 / LogL: -21152.657 / Time: 0h:0m:4s (0h:0m:7s left)
+Iteration 50 / LogL: -21157.765 / Time: 0h:0m:5s (0h:0m:5s left)
+Iteration 60 / LogL: -21152.793 / Time: 0h:0m:6s (0h:0m:4s left)
+Iteration 70 / LogL: -21152.521 / Time: 0h:0m:6s (0h:0m:3s left)
+Iteration 80 / LogL: -21152.804 / Time: 0h:0m:7s (0h:0m:1s left)
+Iteration 90 / LogL: -21152.537 / Time: 0h:0m:8s (0h:0m:0s left)
+Iteration 100 / LogL: -21152.644 / Time: 0h:0m:8s (0h:0m:0s left)
+TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:8s
 
 --------------------------------------------------------------------
 |                    FINALIZING TREE SEARCH                        |
 --------------------------------------------------------------------
 Performs final model parameters optimization
 Estimate model parameters (epsilon = 0.010)
-1. Initial log-likelihood: -11222.774
-Optimal log-likelihood: -11222.772
-Rate parameters:  A-C: 1.51945  A-G: 2.61626  A-T: 1.67742  C-G: 1.98643  C-T: 2.61626  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 (0.188 sec)
-BEST SCORE FOUND : -11222.772
-Total tree length: 12.603
-
-Total number of iterations: 160
-CPU time used for tree search: 93.506 sec (0h:1m:33s)
-Wall-clock time used for tree search: 231.530 sec (0h:3m:51s)
-Total CPU time used: 97.340 sec (0h:1m:37s)
-Total wall-clock time used: 240.909 sec (0h:4m:0s)
+1. Initial log-likelihood: -21152.511
+Optimal log-likelihood: -21152.507
+Rate parameters:  A-C: 5.70686  A-G: 7.79923  A-T: 5.70686  C-G: 1.00000  C-T: 23.13277  G-T: 1.00000
+Base frequencies:  A: 0.355  C: 0.228  G: 0.192  T: 0.225
+Proportion of invariable sites: 0.154
+Gamma shape alpha: 0.728
+Parameters optimization took 1 rounds (0.018 sec)
+BEST SCORE FOUND : -21152.507
+Total tree length: 4.225
+
+Total number of iterations: 102
+CPU time used for tree search: 7.261 sec (0h:0m:7s)
+Wall-clock time used for tree search: 7.338 sec (0h:0m:7s)
+Total CPU time used: 8.786 sec (0h:0m:8s)
+Total wall-clock time used: 8.867 sec (0h:0m:8s)
 
 Analysis results written to: 
   IQ-TREE report:                example.phy.iqtree
@@ -10887,12 +10870,14 @@
   Likelihood distances:          example.phy.mldist
   Screen log file:               example.phy.log
 
-Date and Time: Tue Nov  5 18:11:55 2024
-106.73user 1.08system 4:28.78elapsed 40%CPU (0avgtext+0avgdata 14476maxresident)k
-40inputs+512outputs (1major+4503minor)pagefaults 0swaps
-+ rm -rf /tmp/iqtree-test.WONLEt
-210.41user 2.54system 9:07.53elapsed 38%CPU (0avgtext+0avgdata 14476maxresident)k
-10928inputs+1104outputs (74major+11449minor)pagefaults 0swaps
+Date and Time: Mon Dec  8 23:53:05 2025
+
+real	0m14.875s
+user	0m14.725s
+sys	0m0.148s
++ rm -rf /tmp/iqtree-test.YEa4XK
+29.60user 0.32system 0:29.92elapsed 99%CPU (0avgtext+0avgdata 16264maxresident)k
+0inputs+328outputs (0major+6362minor)pagefaults 0swaps
 rm example.short
 make[1]: Leaving directory '/build/reproducible-path/iqtree-2.0.7+dfsg'
    create-stamp debian/debhelper-build-stamp
@@ -10901,7 +10886,7 @@
 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"
+	cd build.serial && make -j42 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
@@ -10919,7 +10904,7 @@
 -- 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"
+	cd build.mpi && make -j42 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
@@ -10991,12 +10976,14 @@
 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/1465381/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1465381/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/306718 and its subdirectories
-I: Current time: Tue Nov  5 06:18:06 -12 2024
-I: pbuilder-time-stamp: 1730830686
+I: removing directory /srv/workspace/pbuilder/1465381 and its subdirectories
+I: Current time: Tue Dec  9 13:54:43 +14 2025
+I: pbuilder-time-stamp: 1765238083