Diff of the two buildlogs:

--
--- b1/build.log	2025-03-18 12:06:07.363883598 +0000
+++ b2/build.log	2025-03-18 12:09:02.359982591 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Mon Mar 17 23:56:14 -12 2025
-I: pbuilder-time-stamp: 1742298974
+I: Current time: Tue Apr 21 08:29:09 +14 2026
+I: pbuilder-time-stamp: 1776709749
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -26,52 +26,84 @@
 dpkg-source: info: applying remove_test_likelihood_nh.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/505497/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3774404/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 Apr 20 18:29 /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/3774404/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3774404/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='trixie'
-  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]="37" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.37(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=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='f21d65a9dfdb441eacd9c2198a9b956b'
-  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='505497'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=dc7bc394b81d4d568a94cfdd3ff02ba6
+  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=3774404
   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.qmv8yuzC/pbuilderrc_MXxS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qmv8yuzC/b1 --logfile b1/build.log libbpp-phyl_2.4.1-11.dsc'
-  SUDO_GID='111'
-  SUDO_UID='106'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://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.qmv8yuzC/pbuilderrc_hJqn --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.qmv8yuzC/b2 --logfile b2/build.log libbpp-phyl_2.4.1-11.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 ionos11-amd64 6.1.0-32-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.129-1 (2025-03-06) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.12.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.12-1~bpo12+1 (2025-02-23) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Mar  4 11:20 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/505497/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Mar  4  2025 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/3774404/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -178,7 +210,7 @@
 Get: 63 http://deb.debian.org/debian trixie/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB]
 Get: 64 http://deb.debian.org/debian trixie/main amd64 libbpp-seq12t64 amd64 2.4.1-13 [510 kB]
 Get: 65 http://deb.debian.org/debian trixie/main amd64 libbpp-seq-dev amd64 2.4.1-13 [745 kB]
-Fetched 43.6 MB in 2s (23.6 MB/s)
+Fetched 43.6 MB in 1s (77.2 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package libproc2-0:amd64.
 (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 ... 19785 files and directories currently installed.)
@@ -453,7 +485,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && 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  > ../libbpp-phyl_2.4.1-11_source.changes
+I: user script /srv/workspace/pbuilder/3774404/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/3774404/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/libbpp-phyl-2.4.1/ && 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  > ../libbpp-phyl_2.4.1-11_source.changes
 dpkg-buildpackage: info: source package libbpp-phyl
 dpkg-buildpackage: info: source version 2.4.1-11
 dpkg-buildpackage: info: source distribution unstable
@@ -493,7 +529,7 @@
 --   shared lib: /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0
 --   includes: /usr/include
 -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
--- Configuring done (0.8s)
+-- Configuring done (0.6s)
 -- Generating done (0.4s)
 CMake Warning:
   Manually-specified variables were not used by the project:
@@ -505,7 +541,7 @@
 
 -- Build files have been written to: /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu
    dh_auto_build
-	cd obj-x86_64-linux-gnu && make -j20 "INSTALL=install --strip-program=true" VERBOSE=1
+	cd obj-x86_64-linux-gnu && make -j42 "INSTALL=install --strip-program=true" VERBOSE=1
 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
@@ -514,231 +550,249 @@
 make  -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/depend
 make  -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/depend
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake "--color="
-make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake "--color="
-make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-make  -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 make  -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[  0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
+[  0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
+[  0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
+[  0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
+[  0%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o
+[  0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o
+[  1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
 [  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionTools.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
+[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
 [  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/BioNJ.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/BioNJ.cpp
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
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-[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
-[  5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
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+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp
-[  5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
-[  6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
-[  6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o
+[  5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/PGMA.cpp
-[  6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
-[  6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/HierarchicalClustering.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
+[  7%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp
+[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
+[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
+[  9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
+[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
+[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
+[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/CladogramPlot.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/PhylogramPlot.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Graphics/TreeDrawingListener.cpp
-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp
-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp
-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp
-[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppORateDistributionFormat.cpp
-[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp
 [ 11%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp
-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp
-[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp
+[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp
-[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp
-[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp
-[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
+[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
-[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
+[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp
+[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
-[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
+[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp
+[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
+[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp
+[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp
+[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp
+[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp
+[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
+[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
+[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp
-[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o
+[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp
-[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp
-[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o
+[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp
-[ 15%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp
-[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/IoTreeFactory.cpp
-[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Newick.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Newick.cpp
-[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
+[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
+[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp
+[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
+[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/NexusIoTree.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
+[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
+[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
+[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
+[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
+[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Io/Nhx.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
+[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
+[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
+[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
-[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.cpp.o
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-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
+[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp
-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp
-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
+[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
+[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
-[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp
-[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
+[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
+[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
+[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
+[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
+[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp
-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
+[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
-[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp
-[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp
-[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
-[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
-[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
+[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
+[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
+[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
+[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
+[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp
+[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp
-[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp
-[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
+[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp
-[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp
-[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
+[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
+[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp
+[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
+[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionMethods.cpp
+[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
+[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
+[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
+[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
+[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionMethods.cpp
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
-[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o
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-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
+[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp
+[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
 In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
                  from /usr/include/c++/14/bits/allocator.h:46,
                  from /usr/include/c++/14/vector:63,
@@ -765,84 +819,46 @@
 /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)'
   151 |         return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
       |                                                       ^
-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp
-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
-[ 30%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
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-[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o
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-[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o
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-[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
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-[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
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-[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp
-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp
-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp
-[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
-[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o
-[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
-[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
-[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/GY94.cpp
+[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionReward.cpp
+[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
+[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
+[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp
+[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
+[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
+[ 33%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp
+[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp
+[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
+[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp
+[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
+[ 35%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.cpp
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/NaiveSubstitutionCount.cpp
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.cpp
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.cpp
+[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.cpp
+[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
+[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp
 In file included from /usr/include/x86_64-linux-gnu/c++/14/bits/c++allocator.h:33,
                  from /usr/include/c++/14/bits/allocator.h:46,
                  from /usr/include/c++/14/vector:63,
@@ -869,490 +885,513 @@
 /usr/include/c++/14/bits/new_allocator.h:151:55: note: returned from 'void* operator new(std::size_t)'
   151 |         return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp)));
       |                                                       ^
-[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/RewardMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/RewardMappingTools.cpp
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionMappingTools.cpp
+[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
-[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o
+[ 38%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/SubstitutionRegister.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/SubstitutionRegister.cpp
+[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.cpp
+[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Mapping/WeightedSubstitutionCount.cpp
+[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp
-[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o
+[ 39%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp
+[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp
-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp
-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp
-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp
-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o
+[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp
-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
+[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
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-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o
+[ 41%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp
-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.cpp
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.cpp
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.cpp
+[ 42%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
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-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
+[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp
+[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
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-[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o
+[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/AbstractWordSubstitutionModel.cpp
+[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/BinarySubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/BinarySubstitutionModel.cpp
+[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp
-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o
+[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o
+[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
+[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp
+[ 44%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp
-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RE08.cpp
-[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
+[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.cpp
+[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.cpp
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/GY94.cpp
-[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp
-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o
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-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
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-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
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-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.cpp
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o
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-[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o
+[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.cpp
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp
-[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp
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-[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp
-[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.cpp
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.cpp
+[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp
+[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp
-[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
-[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
-[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
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-[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp
-[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
+[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YN98.cpp
-[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp
-[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp
-[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp
-[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
+[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp
+[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.cpp
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.cpp
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.cpp
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp
-[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
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-[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp
+[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp
-[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp
-[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
+[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp
-[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp
-[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
+[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/GY94.cpp
+[ 52%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp
-[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
+[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KCM.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KCM.cpp
+[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.cpp
+[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
+[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp
-[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.cpp
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
+[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp
-[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp
-[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/MG94.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/SENCA.cpp
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp
-[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp
-[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YN98.cpp
+[ 55%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp
-[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
+[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M1.cpp
+[ 56%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp
-[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
+[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp
-[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
+[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M10.cpp
+[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp
-[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
+[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp
-[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
+[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M2.cpp
+[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
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-[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
+[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp
-[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
+[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
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-[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
+[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M3.cpp
+[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M7.cpp
+[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M8.cpp
+[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/YNGP_M9.cpp
+[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp
-[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
+[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp
-[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
+[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
-[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
+[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp
-[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
+[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp
+[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp
-[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
-[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp
-[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp
+[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp
+[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp
+[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp
-[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp
-[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp
-[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp
-[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp
-[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
+[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp
+[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/F84.cpp
+[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp
-[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
+[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp
-[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o
+[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/GTR.cpp
+[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/HKY85.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/HKY85.cpp
+[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp
-[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o
+[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp
-[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o
+[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp
-[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o
+[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp
+[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/K80.cpp
+[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
+[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/L95.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95.cpp
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/RN95s.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/RN95s.cpp
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp
-[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/SSR.cpp
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/T92.cpp
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp
-[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
+[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
-[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/TN93.cpp
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/YpR.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/YpR.cpp
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/gBGC.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Nucleotide/gBGC.cpp
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp
-[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp
-[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeTransitionModel.cpp
+[ 72%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp
-[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o
+[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp
-[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
-[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.cpp
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
-[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/Coala.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/Coala.cpp
+[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
-[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
+[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/CoalaCore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/CoalaCore.cpp
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/DSO78.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/DSO78.cpp
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JCprot.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JCprot.cpp
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/JTT92.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/JTT92.cpp
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
-[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG08.cpp
+[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LG10_EX_EHO.cpp
+[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LGL08_CAT.cpp
+[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EHO.cpp
+[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX2.cpp
+[ 77%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp
+[ 78%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
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-[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
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-[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
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 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
-[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
+[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp
+[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp
-[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o
+[ 80%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RE08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RE08.cpp
-[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp
-[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp
-[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Protein/WAG01.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/WAG01.cpp
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
-[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
+[ 81%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RE08.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RE08.cpp
+[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
-[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
+[ 82%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.cpp
+[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/StateMap.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/StateMap.cpp
+[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp
-[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o
+[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp
-yl/Model/SubstitutionModelSet.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/SitePatterns.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeExceptions.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTemplateTools.cpp.o" "CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/TreeTools.cpp.o"  /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbpp-phyl.so.12.0.0 libbpp-phyl.so.12 libbpp-phyl.so
-make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 88%] Built target bpp-phyl-shared
-[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o
+[ 83%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp
-[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o
+[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp
-[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
+[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
-[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
+[ 84%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
-[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp
-[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp
-[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSet.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSet.cpp
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/SubstitutionModelSetTools.cpp
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/WordSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/WordSubstitutionModel.cpp
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PhyloStatistics.cpp
-make  -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color="
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-[ 91%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp
-[ 91%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
+[ 85%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/MutationProcess.cpp
-[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
+[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
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-[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o
+[ 86%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o
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-[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o
+[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/NNITopologySearch.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/NNITopologySearch.cpp
+[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/SitePatterns.cpp
-[ 92%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o
+[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Node.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Node.cpp
+[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/OptimizationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/OptimizationTools.cpp
+[ 87%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeExceptions.cpp
-[ 93%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
+[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.cpp
+[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyData.cpp
+[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.cpp
+[ 88%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PatternTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/PatternTools.cpp
+[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
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-[ 93%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o
+[ 89%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTools.cpp
+[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/PhyloStatistics.cpp.o
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+[ 90%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Simulation/MutationProcess.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp
-make  -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/depend
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_detailed_simulations.dir/DependInfo.cmake "--color="
+make  -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/depend
+make  -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
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-make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood.cpp
-make  -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/depend
+make  -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/depend
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
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-[ 94%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp
-make  -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/depend
+make  -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/depend
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
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-make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
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-[ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp
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-[ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp
-make  -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/depend
+make  -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend
+make  -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_models.dir/test_models.cpp.o -MF CMakeFiles/test_models.dir/test_models.cpp.o.d -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_models.cpp
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+make  -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend
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-[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o
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-make  -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/depend
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+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree.dir/DependInfo.cmake "--color="
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake "--color="
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake "--color="
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+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f test/CMakeFiles/test_detailed_simulations.dir/build.make test/CMakeFiles/test_detailed_simulations.dir/build
+make  -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build
+make  -f test/CMakeFiles/test_mapping_codon.dir/build.make test/CMakeFiles/test_mapping_codon.dir/build
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-make  -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-make  -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build
+make  -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 95%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree.cpp
-make  -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build
+make  -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build
+make  -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make  -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build
+make  -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 make  -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp
-make  -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-phyl-2.4.1 /build/reproducible-path/libbpp-phyl-2.4.1/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 make  -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/build
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 96%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+[ 92%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp
+[ 93%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o
+[ 95%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o
+[ 96%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
+[ 96%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o
+[ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_bowker.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -MF CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o.d -o CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood_clock.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_nhx.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -MF CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o.d -o CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_likelihood.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -MF CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o.d -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_simulations.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_parsimony.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_models.dir/test_models.cpp.o -MF CMakeFiles/test_models.dir/test_models.cpp.o.d -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_models.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++  -I/build/reproducible-path/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/test/test_tree.cpp
 [ 96%] Linking CXX executable test_tree_getpath
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_getpath.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_tree_getpath.dir/link.d CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -o test_tree_getpath  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
@@ -1363,76 +1402,73 @@
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_nhx.dir/link.d CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 [ 97%] Built target test_nhx
-[ 97%] Linking CXX executable test_models
+[ 98%] Linking CXX executable test_tree_rootat
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_rootat.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_tree_rootat.dir/link.d CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+[ 98%] Built target test_tree_rootat
+[ 98%] Linking CXX executable test_models
+[ 98%] Linking CXX executable test_parsimony
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_models.dir/link.d CMakeFiles/test_models.dir/test_models.cpp.o -o test_models  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[ 97%] Built target test_models
-[ 97%] Linking CXX executable test_parsimony
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1
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+[ 98%] Built target test_parsimony
+[ 98%] Linking CXX executable test_tree
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+[ 99%] Linking CXX executable test_likelihood
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+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+[100%] Built target test_bowker
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+/usr/bin/ranlib libbpp-phyl.a
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
-[100%] Built target test_mapping
 [100%] Linking CXX executable test_simulations
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_simulations.dir/link.d CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 [100%] Built target test_simulations
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-/usr/bin/ranlib libbpp-phyl.a
-make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+[100%] Linking CXX executable test_mapping
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1
 [100%] Built target bpp-phyl-static
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_mapping.dir/link.d CMakeFiles/test_mapping.dir/test_mapping.cpp.o -o test_mapping  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
+[100%] Built target test_mapping
 make[2]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles 0
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
    dh_auto_test
-	cd obj-x86_64-linux-gnu && make -j20 test ARGS\+=--verbose ARGS\+=-j20
+	cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42
 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 Running tests...
-/usr/bin/ctest --force-new-ctest-process --verbose -j20
+/usr/bin/ctest --force-new-ctest-process --verbose -j42
 UpdateCTestConfiguration  from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl
 Parse Config file:/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl
 UpdateCTestConfiguration  from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl
@@ -1544,39 +1580,6 @@
 3: Done.
 3: Tree scaled by.........................: 8.31477
 3: * likelihood after tree scale..........: 71.6905
-3: 
Optimizing... / 1
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-3: 
-3: 65.72293577215039306338
-3: * likelihood after full optimization...: 65.7229
-3: Testing Double Tree Traversal likelihood class...
-3: Initializing data structure............: Done.
-3: Number of distinct sites...............: 12
-3: Test model.............................: T92
-3: 85.03094203195020384101
-3: * initial likelihood...................: 85.0309
-3: Initial bracketing:
-3: A: x = 0.5, f = 80.2872
-3: B: x = 2.11803, f = 71.6905
-3: C: x = 2.76139, f = 71.7653
-3: Step	scale factor	Function	Time
-3: 0	2.11803	71.690520	0.000000
-3: 
Optimizing... / 11	2.11803	71.690520	0.000000
-3: Done.
-3: Tree scaled by.........................: 8.31477
-3: * likelihood after tree scale..........: 71.6905
-3: 
Optimizing... / 1
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-3: 
-3: 65.72293577215069149133
-3: * likelihood after full optimization...: 65.7229
-3: Initializing data structure............: Done.
-3: Number of distinct sites...............: 12
-3: Initializing data structure............: Done.
-3: Number of distinct sites...............: 12
-3: BrLen0	-212.54368339472844695592	-212.54368339472844695592
-3: BrLen1	-107.42239645667785907790	-107.42239645667787328875
-3: BrLen2	3.41183634475365238359	3.41183634475364838679
-3: BrLen3	-187.23500312051925220658	-187.23500312051925220658
-3: BrLen4	-56.02595035016005198258	-56.02595035016005908801
 4: 
/ 1
- 2
\ 3
- 4
/ 5
- 6
\ 7 nodes loaded.
 4: Initializing data structure............: Done.
 4: Number of distinct sites...............: 14
@@ -1593,21 +1596,18 @@
 5: [0.0518135, 0.906736, 0.272021, -1.23057]
 5: ]
 6: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
+ 1/13 Test  #8: test_nhx .........................   Passed    0.01 sec
 9: Initializing data structure............: Done.
 9: Number of distinct sites...............: 9
 9: Parsimony score: 9
+ 2/13 Test  #9: test_parsimony ...................   Passed    0.01 sec
 10: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
-10: Theta0 set to 0.0277909
-10: Theta1 set to 0.514047
-10: Theta2 set to 0.868939
-10: Theta3 set to 0.873698
-10: Theta4 set to 0.760528
+10: Theta0 set to 0.0112736
+10: Theta1 set to 0.249611
+10: Theta2 set to 0.737016
+10: Theta3 set to 0.232386
+10: Theta4 set to 0.611696
 10: Fast check:
- 1/13 Test  #3: test_likelihood ..................   Passed    0.51 sec
- 2/13 Test  #7: test_models ......................   Passed    0.23 sec
- 3/13 Test  #8: test_nhx .........................   Passed    0.21 sec
- 4/13 Test  #9: test_parsimony ...................   Passed    0.19 sec
-13: Total length...........................: 97.7309
 12: 
/ 1
- 2
\ 3
- 4
/ 5 nodes loaded.
 12: Id node1 0
 12: Id node2 1
@@ -1623,7 +1623,7 @@
 12: 4
 12: 3
 12: 2
- 5/13 Test #12: test_tree_getpath ................   Passed    0.22 sec
+ 3/13 Test #12: test_tree_getpath ................   Passed    0.01 sec
 4: 
Optimizing... / 1
Optimizing... - 2
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 4: 
 4: 71.26579958637299228
@@ -1638,7 +1638,43 @@
 4: BrLen5	0.448312	[ 1e-06; 10000] 
 4: T92.kappa	0.996464	]0; +inf[
 4: T92.theta	0.579955	]1e-06; 0.999999[
- 6/13 Test #13: test_tree_rootat .................   Passed    0.44 sec
+13: Total length...........................: 100.448
+3: 
Optimizing... / 1
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Optimizing... \ 31
+3: 
+3: 65.72293577215015147885
+3: * likelihood after full optimization...: 65.7229
+3: Testing Double Tree Traversal likelihood class...
+3: Initializing data structure............: Done.
+3: Number of distinct sites...............: 12
+3: Test model.............................: T92
+3: 85.03094203195020384101
+3: * initial likelihood...................: 85.0309
+3: Initial bracketing:
+3: A: x = 0.5, f = 80.2872
+3: B: x = 2.11803, f = 71.6905
+3: C: x = 2.76139, f = 71.7653
+3: Step	scale factor	Function	Time
+3: 0	2.11803	71.690520	0.000000
+3: 
Optimizing... / 11	2.11803	71.690520	0.000000
+3: Done.
+3: Tree scaled by.........................: 8.31477
+3: * likelihood after tree scale..........: 71.6905
+ 4/13 Test  #7: test_models ......................   Passed    0.04 sec
+3: 
Optimizing... / 1
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+3: 
+3: 65.72293577215069149133
+3: * likelihood after full optimization...: 65.7229
+3: Initializing data structure............: Done.
+3: Number of distinct sites...............: 12
+3: Initializing data structure............: Done.
+3: Number of distinct sites...............: 12
+3: BrLen0	-212.54368339472844695592	-212.54368339472844695592
+3: BrLen1	-107.42239645667785907790	-107.42239645667787328875
+3: BrLen2	3.41183634475365238359	3.41183634475364838679
+3: BrLen3	-187.23500312051925220658	-187.23500312051925220658
+3: BrLen4	-56.02595035016005198258	-56.02595035016005908801
+ 5/13 Test  #3: test_likelihood ..................   Passed    0.05 sec
+ 6/13 Test #13: test_tree_rootat .................   Passed    0.07 sec
 4: Initializing data structure............: Done.
 4: Number of distinct sites...............: 14
 4: Test model.............................: T92
@@ -1646,7 +1682,7 @@
 4: * initial likelihood...................: 92.3295
 4: 
Optimizing... / 1
Optimizing... \ 15
Optimizing... - 22
Optimizing... / 29
Optimizing... / 37
Optimizing... / 45
Optimizing... - 52
Optimizing... \ 59
Optimizing... \ 67
Optimizing... \ 75
Optimizing... / 81
Optimizing... - 88
Optimizing... \ 95
Optimizing... \ 103
Optimizing... - 110
Optimizing... - 116
Optimizing... - 124
Optimizing... \ 131
Optimizing... \ 139
Optimizing... \ 147
 4: 
-4: 71.26579406919543657750
+4: 71.26579406919438497425
 4: * likelihood after full optimization...: 71.2658
 4: Name:	Value:	Constraint:
 4: _________________________________________________
@@ -1655,54 +1691,13 @@
 4: HeightP2	0.819072	[ 0; 1] 
 4: T92.kappa	0.996398	]0; +inf[
 4: T92.theta	0.579960	]1e-06; 0.999999[
+ 7/13 Test  #4: test_likelihood_clock ............   Passed    0.14 sec
 10: Initializing data structure............: Done.
-10: Number of distinct sites...............: 195
- 7/13 Test  #4: test_likelihood_clock ............   Passed    1.36 sec
-2: Br0 BrLen = 0.001 counts = 0.00105
-2: 4x4
-2: [
-2: [0, 4e-05, 0.0001, 1e-05]
-2: [4e-05, 0, 0.0001, 0.00024]
-2: [9e-05, 0.00011, 0, 2e-05]
-2: [0, 0.00024, 6e-05, 0]
-2: ]
-2: Br1 BrLen = 0.002 counts = 0.00211
-2: 4x4
-2: [
-2: [0, 0.0001, 0.0002, 3e-05]
-2: [7e-05, 0, 0.00028, 0.0003]
-2: [0.00021, 0.0002, 0, 0.00013]
-2: [3e-05, 0.00035, 0.00021, 0]
-2: ]
-2: Br2 BrLen = 0.003 counts = 0.003
-2: 4x4
-2: [
-2: [0, 7e-05, 0.00024, 4e-05]
-2: [0.00012, 0, 0.00036, 0.00052]
-2: [0.00031, 0.00042, 0, 0.00018]
-2: [7e-05, 0.00052, 0.00015, 0]
-2: ]
-2: Br3 BrLen = 0.01 counts = 0.0097
-2: 4x4
-2: [
-2: [0, 0.00032, 0.00093, 9e-05]
-2: [0.00034, 0, 0.00125, 0.00183]
-2: [0.00095, 0.00116, 0, 0.00052]
-2: [7e-05, 0.00172, 0.00052, 0]
-2: ]
-2: Br4 BrLen = 0.1 counts = 0.10068
-2: 4x4
-2: [
-2: [0, 0.00367, 0.0091, 0.00107]
-2: [0.00359, 0, 0.01236, 0.01797]
-2: [0.00857, 0.01307, 0, 0.00574]
-2: [0.00108, 0.01871, 0.00575, 0]
-2: ]
- 8/13 Test  #2: test_detailed_simulations ........   Passed    2.43 sec
+10: Number of distinct sites...............: 185
 5: 
[                                      ]   0%
[=                                     ]   2%
[==                                    ]   5%
[===                                   ]   7%
[====                                  ]  10%
[=====                                 ]  13%
[======                                ]  15%
[=======                               ]  18%
[========                              ]  21%
[=========                             ]  23%
[==========                            ]  26%
[===========                           ]  28%
[============                          ]  31%
[=============                         ]  34%
[==============                        ]  36%
[===============                       ]  39%
[================                      ]  42%
[=================                     ]  44%
[==================                    ]  47%
[===================                   ]  50%
[====================                  ]  52%
[=====================                 ]  55%
[======================                ]  57%
[=======================               ]  60%
[========================              ]  63%
[=========================             ]  65%
[==========================            ]  68%
[===========================           ]  71%
[============================          ]  73%
[=============================         ]  76%
[==============================        ]  78%
[===============================       ]  81%
[================================      ]  84%
[=================================     ]  86%
[==================================    ]  89%
[===================================   ]  92%
[====================================  ]  94%
[===================================== ]  97%
[======================================] 100%Done.
 5: Initializing data structure............: Done.
 5: Number of distinct sites...............: 76
-5: 77003.5
+5: 77500.9
 5: Analytical (Laplace) total count:
 5: 4x4
 5: [
@@ -1731,6 +1726,47 @@
 5: [0, 0, 0, 0]
 5: [0, 0, 0, 0]
 5: ]
+2: Br0 BrLen = 0.001 counts = 0.00102
+2: 4x4
+2: [
+2: [0, 1e-05, 2e-05, 0]
+2: [1e-05, 0, 0.00015, 0.00023]
+2: [0.00013, 0.00011, 0, 7e-05]
+2: [2e-05, 0.00022, 5e-05, 0]
+2: ]
+2: Br1 BrLen = 0.002 counts = 0.00192
+2: 4x4
+2: [
+2: [0, 5e-05, 0.00018, 2e-05]
+2: [8e-05, 0, 0.00021, 0.00028]
+2: [0.00024, 0.00029, 0, 0.00011]
+2: [2e-05, 0.00037, 7e-05, 0]
+2: ]
+2: Br2 BrLen = 0.003 counts = 0.00313
+2: 4x4
+2: [
+2: [0, 7e-05, 0.00031, 5e-05]
+2: [9e-05, 0, 0.00042, 0.00059]
+2: [0.00028, 0.00035, 0, 0.00012]
+2: [5e-05, 0.00059, 0.00021, 0]
+2: ]
+2: Br3 BrLen = 0.01 counts = 0.01042
+2: 4x4
+2: [
+2: [0, 0.00051, 0.0009, 4e-05]
+2: [0.00039, 0, 0.0011, 0.00208]
+2: [0.00104, 0.00146, 0, 0.0004]
+2: [7e-05, 0.00186, 0.00057, 0]
+2: ]
+2: Br4 BrLen = 0.1 counts = 0.09921
+2: 4x4
+2: [
+2: [0, 0.00353, 0.00914, 0.00096]
+2: [0.00369, 0, 0.01279, 0.01772]
+2: [0.00914, 0.0122, 0, 0.00568]
+2: [0.00093, 0.01815, 0.00528, 0]
+2: ]
+ 8/13 Test  #2: test_detailed_simulations ........   Passed    0.50 sec
 5: Compute joint node-pairs likelihood....: 
 5: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 5: Total count, decomposition method:
@@ -1846,14 +1882,7 @@
 5: [0.277113, 0.364216, 0.278181, 0.312009]
 5: ]
 5: 6.25012
-5: A	0.001	49	48.3345	48.2968	48.2968	48.3345	48.3345	48.3345	48.3345
-5: B	0.002	109	108.956	108.794	108.794	108.956	108.956	108.956	108.956
-5: 0.008	383	386.074	383.556	383.556	386.074	386.074	386.074	386.074
-5: C	0.01	501	498.886	495.032	495.032	498.886	498.886	498.886	498.886
-5: D	0.02	973	979.265	964.349	964.349	979.265	979.265	979.265	979.265
-5: A	0.001	1.00356/1	1.00438/1	1.00438/1	7.00328/7	7.00658/7	7.00658/7	0.000244382/0	0.000953585/0	0.000953585/0	2.98375/3	2.98451/3	2.98451/3	
-5: B	0.002	2.01753/2	2.0241/2	2.0241/2	10.0164/10	10.0349/10	10.0349/10	1.00171/1	1.00116/1	1.00116/1	2.99771/3	3.00201/3	3.00201/3	
-5: 0.008	8.87208/8	9.00419/8	9.00419/8	29.0906/31	29.385/31	29.385/31	8.94138/9	8.86651/9	8.86651/9	16.9927/18	17.0498/18	17.0498/18	
+5: A	0.001	59	58.5913	58.5496	58.5496	58.5913	58.5913	58.5913	58.5913
 11: 
/ 1
- 2
\ 3
- 4
/ 5 nodes loaded.
 11: ((A:1,B:2):3,C:4);
 11: 
@@ -1882,11 +1911,18 @@
 11: Node 3:
 11: Node 4:
 11: B: ESS=2
-5: C	0.01	17.1789/16	17.2847/16	17.2847/16	46.2092/47	46.6442/47	46.6442/47	4.01192/4	4.01678/4	4.01678/4	16.2819/16	16.4286/16	16.4286/16	
+5: B	0.002	109	109.882	109.718	109.718	109.882	109.882	109.882	109.882
 11: Newick I/O ok.
-5: D	0.02	31.1534/32	31.4928/32	31.4928/32	77.69/82	79.3685/82	79.3685/82	5.45632/5	5.55354/5	5.55354/5	34.2528/36	34.683/36	34.683/36	
- 9/13 Test  #5: test_mapping .....................   Passed    5.24 sec
-1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0387	0.0059
+5: 0.008	433	441.304	438.773	438.773	441.304	441.304	441.304	441.304
+5: C	0.01	517	512.757	508.893	508.893	512.757	512.757	512.757	512.757
+5: D	0.02	1009	1007.44	992.306	992.306	1007.44	1007.44	1007.44	1007.44
+5: A	0.001	2.00743/2	2.00825/2	2.00825/2	8.01909/8	8.02339/8	8.02339/8	0.00145261/0	0.00234307/0	0.00234307/0	1.99061/2	1.99217/2	1.99217/2	
+5: B	0.002	3.01256/3	3.01686/3	3.01686/3	11.0889/11	11.106/11	11.106/11	0.00193908/0	0.00476361/0	0.00476361/0	4.99652/5	5.00485/5	5.00485/5	
+5: 0.008	18.1986/18	18.2747/18	18.2747/18	49.9815/50	50.2945/50	50.2945/50	6.99913/7	6.95631/7	6.95631/7	18.9848/19	19.0157/19	19.0157/19	
+5: C	0.01	19.4608/21	19.577/21	19.577/21	42.6544/43	43.1026/43	43.1026/43	5.59929/6	5.57978/6	5.57978/6	22.9073/23	22.9449/23	22.9449/23	
+5: D	0.02	27.8159/29	28.3001/29	28.3001/29	109.123/112	110.798/112	110.798/112	8.00571/7	8.00344/7	8.00344/7	36.8879/38	37.3854/38	37.3854/38	
+ 9/13 Test  #5: test_mapping .....................   Passed    1.28 sec
+1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.041	0.0062
 1: ..:: Testing with homogeneous, non-stationary model ::..
 11: Newick multiple I/O ok.
 11: Testing parsing a directory...
@@ -1917,13 +1953,21 @@
 11: 
/ 1
- 2
\ 3 nodes loaded.
 11: ((A:1):2);
 11: 
-10/13 Test #11: test_tree ........................   Passed   12.30 sec
-1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0416	0.0063
+10/13 Test #11: test_tree ........................   Passed    3.38 sec
+1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0451	0.0064
 1: ..:: Testing with non-homogeneous, non-stationary model ::..
 6: 
[                                      ]   0%
[=                                     ]   2%
[==                                    ]   5%
[===                                   ]   7%
[====                                  ]  10%
[=====                                 ]  13%
[======                                ]  15%
[=======                               ]  18%
[========                              ]  21%
[=========                             ]  23%
[==========                            ]  26%
[===========                           ]  28%
[============                          ]  31%
[=============                         ]  34%
[==============                        ]  36%
[===============                       ]  39%
[================                      ]  42%
[=================                     ]  44%
[==================                    ]  47%
[===================                   ]  50%
[====================                  ]  52%
[=====================                 ]  55%
[======================                ]  57%
[=======================               ]  60%
[========================              ]  63%
[=========================             ]  65%
[==========================            ]  68%
[===========================           ]  71%
[============================          ]  73%
[=============================         ]  76%
[==============================        ]  79%
[===============================       ]  81%
[================================      ]  84%
[=================================     ]  86%
[==================================    ]  89%
[===================================   ]  92%
[====================================  ]  94%
[===================================== ]  97%
[======================================] 100%Done.
 6: Initializing data structure............: Done.
-6: Number of distinct sites...............: 1006
-6: 96426.7
+6: Number of distinct sites...............: 997
+6: 96070.1
+10: 
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
Optimizing... - 10
Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
Optimizing... - 14
Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
Optimizing... - 18
Optimizing... \ 19
Optimizing... - 20
Optimizing... / 21
Optimizing... - 22
+10: 
+10: 0.0112736	0.0143254
+10: 0.249611	0.232813
+10: 0.737016	0.746519
+10: 0.232386	0.241696
+10: 0.611696	0.608374
+10: Detailed check:
 6: Analytical total count:
 6: 64x64
 6: [
@@ -1993,6 +2037,8 @@
 6: [3.00169, 3.00145, 3.00139, 2.00023, 3.00149, 3.00181, 3.00139, 2.00023, 3.00136, 3.0016, 3.00152, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00144, 3.0014, 3.00135, 2.00023, 3.00092, 3.00161, 3.00111, 2.00023, 3.00164, 3.00171, 3.0018, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00157, 3.00128, 3.00143, 2.00023, 3.00155, 3.0017, 3.00158, 2.00023, 3.00136, 3.0013, 3.00154, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, -nan, 2.00015, -nan, 1.00012, 2.00015, 2.00023, 2.00019, 1.00012, -nan, 2.00019, 2.00015, 1.00012, 1.00012, 1.00012, 1.00012, 1.21058e-07]
 6: ]
 6: Compute joint node-pairs likelihood....: 
+10: Initializing data structure............: Done.
+10: Number of distinct sites...............: 195
 6: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 6: Simple total count:
 6: 64x64
@@ -2273,39 +2319,29 @@
 6: [2.75035, 2.00021, 3, 2.00023, 2.3334, 2.00039, 2.49994, 2.00023, 2.74999, 2.00034, 2.99996, 2.00023, 1.50015, 1.00029, 2.00008, 1.00012, 2.50014, 2.00014, 2.50011, 2.00023, 2.16633, 2.00021, 2.16649, 2.00023, 2.00034, 2.0003, 2.33363, 2.00023, 1.00015, 1.00019, 1.00017, 1.00012, 2.75019, 2.00008, 2.7501, 2.00023, 2.33341, 2.0003, 2.33346, 2.00023, 2.2501, 2.00005, 2.50008, 2.00023, 1.5001, 1.00023, 1.50011, 1.00012, 0, 1.00019, 0, 1.00012, 1.50004, 1.00023, 1.50009, 1.00012, 0, 1.00027, 2.00006, 1.00012, 1, 0.000232033, 1, 1.07607e-07]
 6: ]
 6: Compute joint node-pairs likelihood....: 
-1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.932	0.7993
+1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9332	0.8018
 1: ..:: Testing with non-homogeneous, stationary model ::..
 6: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
-11/13 Test  #6: test_mapping_codon ...............   Passed   26.99 sec
-1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0391	0.0064
-12/13 Test  #1: test_bowker ......................   Passed   33.95 sec
-10: 
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
Optimizing... / 9
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Optimizing... \ 11
Optimizing... - 12
Optimizing... / 13
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Optimizing... \ 15
Optimizing... - 16
Optimizing... / 17
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Optimizing... \ 19
Optimizing... - 20
Optimizing... / 21
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Optimizing... - 24
Optimizing... / 25
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Optimizing... \ 27
Optimizing... - 28
Optimizing... / 29
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Optimizing... \ 31
Optimizing... - 32
Optimizing... / 33
Optimizing... - 34
Optimizing... \ 35
Optimizing... - 36
Optimizing... / 37
Optimizing... - 38
Optimizing... \ 39
Optimizing... - 40
Optimizing... / 41
Optimizing... - 42
Optimizing... \ 43
Optimizing... - 44
Optimizing... / 45
Optimizing... - 46
+11/13 Test  #6: test_mapping_codon ...............   Passed    8.59 sec
+1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
[>>>>>>>>>>>>>>                        ]  36%
[>>>>>>>>>>>>>>>                       ]  39%
[>>>>>>>>>>>>>>>>                      ]  42%
[>>>>>>>>>>>>>>>>>                     ]  44%
[>>>>>>>>>>>>>>>>>>                    ]  47%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>                  ]  52%
[>>>>>>>>>>>>>>>>>>>>>                 ]  55%
[>>>>>>>>>>>>>>>>>>>>>>                ]  58%
[>>>>>>>>>>>>>>>>>>>>>>>               ]  60%
[>>>>>>>>>>>>>>>>>>>>>>>>              ]  63%
[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0425	0.0055
+12/13 Test  #1: test_bowker ......................   Passed   11.25 sec
+10: 
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
Optimizing... - 8
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Optimizing... / 17
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Optimizing... - 20
Optimizing... / 21
 10: 
-10: 0.0277909	0.0252228
-10: 0.514047	0.50067
-10: 0.868939	0.86701
-10: 0.873698	0.879105
-10: 0.760528	0.759706
-10: Detailed check:
-10: Initializing data structure............: Done.
-10: Number of distinct sites...............: 201
-10: 
Optimizing... / 1
Optimizing... - 2
Optimizing... \ 3
Optimizing... - 4
Optimizing... / 5
Optimizing... - 6
Optimizing... \ 7
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Optimizing... - 24
Optimizing... / 25
Optimizing... - 26
Optimizing... \ 27
Optimizing... - 28
-10: 
-10: 0.0277909	0.0322587
-10: 0.514047	0.510508
-10: 0.868939	0.860414
-10: 0.873698	0.877646
-10: 0.760528	0.750128
-13/13 Test #10: test_simulations .................   Passed   60.10 sec
+10: 0.0112736	0.0178653
+10: 0.249611	0.268559
+10: 0.737016	0.745041
+10: 0.232386	0.233108
+10: 0.611696	0.613001
+13/13 Test #10: test_simulations .................   Passed   12.54 sec
 
 100% tests passed, 0 tests failed out of 13
 
-Total Test time (real) =  60.73 sec
+Total Test time (real) =  12.55 sec
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
    create-stamp debian/debhelper-build-stamp
    dh_prep
    dh_auto_install
-	cd obj-x86_64-linux-gnu && make -j20 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+	cd obj-x86_64-linux-gnu && make -j42 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
 /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
 make  -f CMakeFiles/Makefile2 preinstall
@@ -2323,237 +2359,237 @@
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-phyl.so
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplate.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RASTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingListener.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractTreeDrawing.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/PhylogramPlot.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/CladogramPlot.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Tree.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PatternTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/AncestralStateReconstruction.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/TreeDrawing.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Graphics/AbstractDendrogramPlot.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/OptimizationTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNITopologySearch.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WrappedModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/InMixedSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WordSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeRegisterTransitionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/TS98.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/BinarySubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSetTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWrappedModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractFromSubstitutionModelTransitionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/ProteinFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RegisterRatesSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractMixedSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/OneChangeTransitionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixedSubstitutionModelSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/WrappedModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/StateMap.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfSubstitutionModels.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/RE08.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/InMixedSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonBGCSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M2.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonPhaseFrequenciesSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KCM.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M1.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M3.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceFrequenciesSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonCpGSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistancePhaseFrequenciesSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M10.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M9.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/GY94.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonDistanceSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YN98.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAAFitnessSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonAdHocSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/SENCA.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/MG94.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MixtureOfASubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/FromMixtureSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWrappedModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/SubstitutionModelSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/G2001.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/AbstractCodonFrequenciesSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M8.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Codon/YNGP_M7.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EHO.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/ProteinSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/DSO78.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL3.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX2.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LGL08_CAT.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JCprot.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG08.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/CoalaCore.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LG10_EX_EHO.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/JTT92.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/Coala.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_EX3.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/WAG01.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Protein/LLG08_UL2.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AbstractWordSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/SSR.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/K80.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/YpR.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/L95.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/F84.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/TN93.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95s.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/gBGC.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/JCnuc.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/T92.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/RN95.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/GTR.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/Nucleotide/HKY85.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/OptimizationTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Model/AnonymousSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Tree.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/ClockTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NonHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/SitePartitionTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RASTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/HomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodData.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihoodTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/TreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Likelihood/AbstractTreeLikelihoodData.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/SitePatterns.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/AncestralStateReconstruction.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Reward.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMapping.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionMethods.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionReward.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionCount.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Mapping.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticRewardMapping.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMappingTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionRegister.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/CategorySubstitutionRegister.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/SubstitutionMappingTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/NaiveSubstitutionCount.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionMethods.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/ProbabilisticSubstitutionMapping.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/Reward.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/OneJumpSubstitutionCount.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/UniformizationSubstitutionCount.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NodeTemplate.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNITopologySearch.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/PhyloStatistics.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/NNISearchable.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/BipartitionList.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/LaplaceSubstitutionCount.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/RewardMapping.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Mapping/WeightedSubstitutionCount.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTemplateTools.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyData.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyScore.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/TreeParsimonyData.h
+-- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyScore.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/AbstractTreeParsimonyData.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Parsimony/DRTreeParsimonyScore.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/HierarchicalClustering.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceMethod.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/BioNJ.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/PGMA.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/DistanceEstimation.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Distance/NeighborJoining.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/App/PhylogeneticsApplicationTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/MutationProcess.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulationTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SequenceSimulator.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/SiteSimulator.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Simulation/DetailedSiteSimulator.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TopologySearch.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeTools.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Node.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/TreeExceptions.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOFrequenciesSetFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrix.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSet.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoPairedSiteLikelihoods.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeReaderFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Newick.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/Nhx.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTree.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOSubstitutionModelFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoTreeFactory.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoDistanceMatrixFactory.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/PhylipDistanceMatrixFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoFrequenciesSetFactory.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/NexusIoTree.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModelFactory.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTransitionModelFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppOTreeWriterFormat.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/IoSubstitutionModel.h
--- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/include/Bpp/Phyl/Io/BppORateDistributionFormat.h
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets.cmake
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets-none.cmake
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu'
@@ -2612,12 +2648,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/3774404/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3774404/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/505497 and its subdirectories
-I: Current time: Tue Mar 18 00:06:06 -12 2025
-I: pbuilder-time-stamp: 1742299566
+I: removing directory /srv/workspace/pbuilder/3774404 and its subdirectories
+I: Current time: Tue Apr 21 08:32:01 +14 2026
+I: pbuilder-time-stamp: 1776709921