Diff of the two buildlogs:

--
--- b1/build.log	2024-05-06 11:28:10.416329752 +0000
+++ b2/build.log	2024-05-06 11:35:47.908856914 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Sun Jun  8 05:45:51 -12 2025
-I: pbuilder-time-stamp: 1749404751
+I: Current time: Tue May  7 01:28:13 +14 2024
+I: pbuilder-time-stamp: 1714994893
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -30,54 +30,86 @@
 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/41215/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/61881/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos2-i386.
+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 May  6 11:28 /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/61881/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/61881/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='i386'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='i386'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+  BASH_VERSION='5.2.21(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=i386
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=i686
+  HOST_ARCH=i386
   IFS=' 	
   '
-  INVOCATION_ID='cdf95abb244841779b2f8352bf0441eb'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
-  LD_PRELOAD='libeatmydata.so'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='41215'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=9f7730fc86ba4a17a79b455d27c5c44c
+  LANG=C
+  LANGUAGE=de_CH:de
+  LC_ALL=C
+  LD_LIBRARY_PATH=/usr/lib/libeatmydata
+  LD_PRELOAD=libeatmydata.so
+  MACHTYPE=i686-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=61881
   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.0rl0SgLc/pbuilderrc_cOG3 --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.0rl0SgLc/b1 --logfile b1/build.log libbpp-phyl_2.4.1-10.dsc'
-  SUDO_GID='112'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://213.165.73.152:3128'
+  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.0rl0SgLc/pbuilderrc_9jZK --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.0rl0SgLc/b2 --logfile b2/build.log libbpp-phyl_2.4.1-10.dsc'
+  SUDO_GID=112
+  SUDO_UID=107
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://46.16.76.132:3128
 I: uname -a
-  Linux ionos16-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Jun  5 15:01 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/41215/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 May  3 08:38 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/61881/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: 57 http://deb.debian.org/debian trixie/main i386 libbpp-core-dev i386 2.4.1-12 [1003 kB]
 Get: 58 http://deb.debian.org/debian trixie/main i386 libbpp-seq12t64 i386 2.4.1-12 [522 kB]
 Get: 59 http://deb.debian.org/debian trixie/main i386 libbpp-seq-dev i386 2.4.1-12 [773 kB]
-Fetched 40.3 MB in 1s (66.8 MB/s)
+Fetched 40.3 MB in 1s (68.7 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libproc2-0:i386.
 (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 ... 19683 files and directories currently installed.)
@@ -429,7 +461,11 @@
 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_2.4.1-10_source.changes
+I: user script /srv/workspace/pbuilder/61881/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/61881/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_2.4.1-10_source.changes
 dpkg-buildpackage: info: source package libbpp-phyl
 dpkg-buildpackage: info: source version 2.4.1-10
 dpkg-buildpackage: info: source distribution unstable
@@ -468,8 +504,8 @@
 --   shared lib: /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0
 --   includes: /usr/include
 -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) 
--- Configuring done (0.3s)
--- Generating done (0.1s)
+-- Configuring done (0.4s)
+-- Generating done (0.2s)
 CMake Warning:
   Manually-specified variables were not used by the project:
 
@@ -480,7 +516,7 @@
 
 -- Build files have been written to: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu
    dh_auto_build
-	cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1
+	cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1
 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
 /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu//CMakeFiles/progress.marks
@@ -489,249 +525,205 @@
 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-i686-linux-gnu'
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake "--color="
-make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src/CMakeFiles/bpp-phyl-static.dir/DependInfo.cmake "--color="
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src/CMakeFiles/bpp-phyl-shared.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+make  -f src/CMakeFiles/bpp-phyl-static.dir/build.make src/CMakeFiles/bpp-phyl-static.dir/build
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
 make  -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build
-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-i686-linux-gnu'
 make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[  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/BipartitionList.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/App/PhylogeneticsApplicationTools.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-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o
-[  2%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[  2%] 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-i686-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 -Wformat -Werror=format-security -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
-[  2%] 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/Distance/BioNJ.cpp.o
+[  1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
+[  1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionList.cpp.o
+[  1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
+[  1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[  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/BipartitionTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/AbstractAgglomerativeDistanceMethod.cpp.o
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/BipartitionTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[  3%] 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-i686-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 -Wformat -Werror=format-security -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
-[  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-i686-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 -Wformat -Werror=format-security -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
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o
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-[  3%] 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-i686-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 -Wformat -Werror=format-security -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
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
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-[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
-[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/BioNJ.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[  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-i686-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 -Wformat -Werror=format-security -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/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.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-i686-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 -Wformat -Werror=format-security -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
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[  5%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
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+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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/DistanceEstimation.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/DistanceEstimation.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/DistanceEstimation.cpp
+[  3%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[  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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
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+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[  7%] 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-i686-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 -Wformat -Werror=format-security -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
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/AbstractTreeDrawing.cpp.o
+[  4%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/HierarchicalClustering.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[  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-i686-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 -Wformat -Werror=format-security -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
-[  7%] 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-i686-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 -Wformat -Werror=format-security -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
-[  7%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o
+[  5%] 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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[  7%] 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-i686-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 -Wformat -Werror=format-security -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
-[  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-i686-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 -Wformat -Werror=format-security -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
-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/PhylogramPlot.cpp.o
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-[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingDisplayControler.cpp.o
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-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
-[  9%] 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-i686-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 -Wformat -Werror=format-security -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
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
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-[  9%] 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-i686-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 -Wformat -Werror=format-security -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
-[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOFrequenciesSetFormat.cpp.o
+[  6%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/PGMA.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-shared.dir/Bpp/Phyl/Graphics/AbstractDendrogramPlot.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[  6%] 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-i686-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 -Wformat -Werror=format-security -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
-[  9%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 10%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeReaderFormat.cpp.o
+[  7%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOMultiTreeWriterFormat.cpp.o
+[  8%] 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-i686-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 -Wformat -Werror=format-security -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
+[  8%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppORateDistributionFormat.cpp.o
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-[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
+[  8%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOSubstitutionModelFormat.cpp.o
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-[ 12%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 12%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
+[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTransitionModelFormat.cpp.o
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-[ 13%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 13%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
+[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeReaderFormat.cpp.o
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-[ 14%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 14%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 14%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
+[  9%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/BppOTreeWriterFormat.cpp.o
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-[ 14%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 14%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoDistanceMatrixFactory.cpp.o
+[  9%] 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-i686-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 -Wformat -Werror=format-security -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
+[  9%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 10%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 16%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
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-[ 16%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 16%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 17%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
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-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
+[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoFrequenciesSetFactory.cpp.o
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-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousMixedTreeLikelihood.cpp.o
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-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
+[ 10%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoPairedSiteLikelihoods.cpp.o
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-[ 17%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
+[ 10%] 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-i686-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 -Wformat -Werror=format-security -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-shared.dir/Bpp/Phyl/Graphics/TreeDrawingListener.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 11%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoSubstitutionModelFactory.cpp.o
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-[ 18%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o
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-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 12%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/IoTreeFactory.cpp.o
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-[ 19%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/NexusIoTree.cpp.o
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-[ 20%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Io/Nhx.cpp.o
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-[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractHomogeneousTreeLikelihood.cpp.o
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 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.cpp.o
+[ 13%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 13%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 14%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/AbstractTreeLikelihood.cpp.o
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASDRTreeLikelihoodData.cpp.o
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRASRTreeLikelihoodData.cpp.o
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 15%] 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-i686-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 -Wformat -Werror=format-security -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/NNIHomogeneousTreeLikelihood.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 16%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 16%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 17%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 17%] 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-i686-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 -Wformat -Werror=format-security -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-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o
+[ 17%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 17%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 17%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o
+[ 18%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
+[ 18%] 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-i686-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 -Wformat -Werror=format-security -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
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o
+[ 19%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 19%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 19%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o
+[ 19%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 19%] 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-i686-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 -Wformat -Werror=format-security -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-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 25%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o
+[ 20%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 20%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 20%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 21%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 26%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
+[ 21%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 21%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o
+[ 21%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 26%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o
+[ 22%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 22%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousMixedTreeLikelihood.cpp.o
+[ 22%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 23%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 27%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.cpp.o
+[ 23%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 27%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousMixedTreeLikelihood.cpp.o
+[ 23%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 28%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp.o
+[ 24%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 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-i686-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 -Wformat -Werror=format-security -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
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/TreeLikelihoodTools.cpp.o
+[ 24%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 24%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 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-i686-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 -Wformat -Werror=format-security -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
-[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o
+[ 24%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 25%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionMethods.cpp.o
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-[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 29%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
+[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionReward.cpp.o
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-[ 30%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 31%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Mapping/DecompositionSubstitutionCount.cpp.o
+[ 26%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 31%] 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-i686-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 -Wformat -Werror=format-security -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/DecompositionSubstitutionCount.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 26%] 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-i686-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 -Wformat -Werror=format-security -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
 In file included from /usr/include/i386-linux-gnu/c++/13/bits/c++allocator.h:33,
                  from /usr/include/c++/13/bits/allocator.h:46,
                  from /usr/include/c++/13/vector:63,
@@ -780,12 +772,104 @@
 /usr/include/c++/13/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)));
       |                                                       ^
-[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 26%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 27%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 27%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 27%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 27%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 28%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 28%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 28%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 28%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 28%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 29%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 30%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 30%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 31%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 32%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 33%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 34%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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/AbstractCodonAARateSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonAARateSubstitutionModel.cpp
+[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 36%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 36%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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/AbstractCodonFitnessSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp
+[ 37%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 37%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 37%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 37%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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/AbstractCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractCodonSubstitutionModel.cpp
+[ 37%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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/AbstractKroneckerCodonSubstitutionModel.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Codon/AbstractKroneckerCodonSubstitutionModel.cpp
+[ 38%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 38%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 38%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 39%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 39%] 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-i686-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 -Wformat -Werror=format-security -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
 In file included from /usr/include/i386-linux-gnu/c++/13/bits/c++allocator.h:33,
                  from /usr/include/c++/13/bits/allocator.h:46,
                  from /usr/include/c++/13/vector:63,
@@ -834,250 +918,98 @@
 /usr/include/c++/13/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)));
       |                                                       ^
-[ 33%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 33%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 33%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 34%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 35%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 36%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 36%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 36%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 36%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/AbstractBiblioMixedSubstitutionModel.cpp.o
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-[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/CodonDistanceSubstitutionModel.cpp.o
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-[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/MG94.cpp.o
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-[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/SENCA.cpp.o
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-[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 40%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/GY94.cpp.o
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
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-[ 53%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/TripletSubstitutionModel.cpp.o
+[ 42%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 42%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 42%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YN98.cpp.o
+[ 43%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M1.cpp.o
+[ 43%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 54%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
+[ 43%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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_M10.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M10.cpp.o.d -o CMakeFiles/bpp-phyl-static.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
-[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 55%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 55%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 55%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M2.cpp.o
+[ 44%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M3.cpp.o
+[ 44%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M7.cpp.o
+[ 44%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 44%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 45%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 45%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 45%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 57%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
+[ 45%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 45%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M8.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 57%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Codon/YNGP_M9.cpp.o
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-[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.cpp.o
-[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/CodonFrequenciesSet.cpp.o
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-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
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-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
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-[ 59%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
+[ 46%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 46%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/MvaFrequenciesSet.cpp.o
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-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
+[ 46%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 47%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/NucleotideFrequenciesSet.cpp.o
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-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
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-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
+[ 48%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 48%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp.o
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-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
+[ 48%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/FromMixtureSubstitutionModel.cpp.o
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-[ 60%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
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-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
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-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
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-[ 61%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
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-[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
+[ 48%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 49%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/InMixedSubstitutionModel.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/KroneckerWordSubstitutionModel.cpp.o
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+[ 50%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o
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-[ 63%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
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+[ 50%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 50%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixedSubstitutionModelSet.cpp.o
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-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
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+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 51%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfASubstitutionModel.cpp.o
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-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/MixtureOfSubstitutionModels.cpp.o
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-[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/F84.cpp.o
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-[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/GTR.cpp.o
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-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 52%] 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-i686-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 -Wformat -Werror=format-security -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
 In file included from /usr/include/i386-linux-gnu/c++/13/bits/c++allocator.h:33,
                  from /usr/include/c++/13/bits/allocator.h:46,
                  from /usr/include/c++/13/string:43,
@@ -1108,14 +1040,198 @@
 /usr/include/c++/13/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)));
       |                                                       ^
-[ 66%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/JCnuc.cpp.o
+[ 53%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 53%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 53%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 67%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 67%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/K80.cpp.o
+[ 53%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 53%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 54%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 55%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 56%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 57%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Codon/AbstractCodonFitnessSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 58%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 59%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 59%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 60%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 60%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 61%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 61%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 61%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 61%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 62%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LG08.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 62%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 62%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 63%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 63%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 63%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 63%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 63%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 64%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 64%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 64%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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_EX3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Model/Protein/LLG08_EX3.cpp
+[ 64%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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_UL2.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL2.cpp.o.d -o CMakeFiles/bpp-phyl-static.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
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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_UL3.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/LLG08_UL3.cpp.o.d -o CMakeFiles/bpp-phyl-static.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
+[ 65%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Model/Protein/UserProteinSubstitutionModel.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 65%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 66%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 66%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 66%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 66%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 67%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 69%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 70%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 70%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/NNITopologySearch.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 70%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Node.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 70%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 71%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/OptimizationTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 71%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 71%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 71%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 72%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 72%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 73%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PatternTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 73%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/PhyloStatistics.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 73%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 73%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 73%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/NonHomogeneousSequenceSimulator.cpp
+[ 74%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/Simulation/SequenceSimulationTools.cpp
+[ 75%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/SitePatterns.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 75%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeExceptions.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 75%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTemplateTools.cpp.o -c /build/reproducible-path/libbpp-phyl-2.4.1/src/Bpp/Phyl/TreeTemplateTools.cpp
+[ 76%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 76%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 76%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/TreeTools.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 77%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 77%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 77%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 78%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 78%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 78%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 78%] 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-i686-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 -Wformat -Werror=format-security -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
 In file included from /usr/include/i386-linux-gnu/c++/13/bits/c++allocator.h:33,
                  from /usr/include/c++/13/bits/allocator.h:46,
                  from /usr/include/c++/13/string:43,
@@ -1146,190 +1262,112 @@
 /usr/include/c++/13/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)));
       |                                                       ^
-[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 68%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/SSR.cpp.o
+[ 79%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 79%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 79%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/L95.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 79%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 80%] 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-i686-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 -Wformat -Werror=format-security -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
+[ 80%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 68%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/T92.cpp.o
+[ 80%] 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-i686-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 -Wformat -Werror=format-security -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
-[ 69%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Model/Nucleotide/TN93.cpp.o
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+make  -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build
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-make  -f test/CMakeFiles/test_likelihood_clock.dir/build.make test/CMakeFiles/test_likelihood_clock.dir/build
 make  -f test/CMakeFiles/test_mapping.dir/build.make test/CMakeFiles/test_mapping.dir/build
-make  -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build
-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
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-make  -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build
+make  -f test/CMakeFiles/test_models.dir/build.make test/CMakeFiles/test_models.dir/build
+make  -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
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+make  -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build
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+make  -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build
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-make  -f test/CMakeFiles/test_likelihood.dir/build.make test/CMakeFiles/test_likelihood.dir/build
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-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-i686-linux-gnu'
-[ 92%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o
+[ 92%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o
 [ 92%] Building CXX object test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o
-[ 92%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o
-[ 92%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 93%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o
-[ 93%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[ 94%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[ 94%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[ 95%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o
+[ 93%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
+[ 94%] Building CXX object test/CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o
+[ 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-i686-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 -Wformat -Werror=format-security -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
-[ 95%] Building CXX object test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o
-[ 96%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o
-[ 96%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
+[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o
+[ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o
+[ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o
+[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o
+[ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
-[ 96%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
-[ 96%] Linking CXX executable test_tree_getpath
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
-make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 96%] Built target test_tree_getpath
-make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 96%] Built target bpp-phyl-static
-[ 97%] Linking CXX executable test_nhx
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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-i686-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 -Wformat -Werror=format-security -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
+[ 96%] Linking CXX executable test_nhx
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_nhx.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 97%] Built target test_nhx
-[ 98%] Linking CXX executable test_tree_rootat
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+[ 96%] Built target test_nhx
+make  -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/depend
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/CMakeFiles/test_tree.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 98%] Built target test_tree_rootat
-[ 98%] Linking CXX executable test_parsimony
+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-i686-linux-gnu'
+[ 96%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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_parsimony
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 98%] Built target test_parsimony
-[ 98%] Linking CXX executable test_tree
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+[ 96%] Built target test_parsimony
+make  -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend
+make[3]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake "--color="
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 98%] Built target test_tree
-[ 98%] Linking CXX executable test_models
+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-i686-linux-gnu'
+[ 97%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 97%] Linking CXX executable test_models
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 98%] Built target test_models
-[ 98%] Linking CXX executable test_likelihood
+[ 97%] Built target test_models
+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-i686-linux-gnu'
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake "--color="
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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-i686-linux-gnu'
+[ 97%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -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
+[ 97%] Linking CXX executable test_likelihood
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
-[ 99%] Linking CXX executable test_likelihood_clock
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+[ 97%] Built target test_likelihood
+[ 98%] Linking CXX executable test_likelihood_clock
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1
 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+[ 98%] Linking CXX executable test_tree_getpath
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 99%] Built target test_likelihood
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 99%] Built target test_likelihood_clock
+[ 98%] Built target test_likelihood_clock
+[ 98%] Built target test_tree_getpath
+[ 99%] Linking CXX executable test_mapping_codon
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 [ 99%] Linking CXX executable test_detailed_simulations
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
-[ 99%] Linking CXX executable test_bowker
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+[ 99%] Built target test_mapping_codon
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
 [ 99%] Built target test_detailed_simulations
+[ 99%] Linking CXX executable test_tree
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[ 99%] Built target test_bowker
-[100%] Linking CXX executable test_mapping_codon
-cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1
-/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+[ 99%] Built target test_tree
+[100%] Linking CXX executable test_tree_rootat
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic 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-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
+[100%] Linking CXX executable test_bowker
+cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1
+/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
 make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
-[100%] Built target test_mapping_codon
+[100%] Built target test_tree_rootat
+make[3]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
+[100%] Built target test_bowker
 [100%] Linking CXX executable test_simulations
 cd /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations  -Wl,-rpath,/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/i386-linux-gnu/libbpp-core.so.4.1.0
@@ -1508,10 +1544,10 @@
 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/CMakeFiles 0
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
    dh_auto_test
-	cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22
+	cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10
 make[1]: Entering directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
 Running tests...
-/usr/bin/ctest --force-new-ctest-process --verbose -j22
+/usr/bin/ctest --force-new-ctest-process --verbose -j10
 UpdateCTestConfiguration  from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/DartConfiguration.tcl
 Parse Config file:/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/DartConfiguration.tcl
 UpdateCTestConfiguration  from :/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/DartConfiguration.tcl
@@ -1583,37 +1619,15 @@
 10: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_simulations
 10: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
 10: Test timeout computed to be: 60000
-test 11
-      Start 11: test_tree
-
-11: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree
-11: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
-11: Test timeout computed to be: 60000
-test 12
-      Start 12: test_tree_getpath
-
-12: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree_getpath
-12: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
-12: Test timeout computed to be: 60000
-test 13
-      Start 13: test_tree_rootat
-
-13: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree_rootat
-13: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
-13: Test timeout computed to be: 60000
-6: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
+10: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
 2: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
 2: 4
-3: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
 4: 
/ 1
- 2
\ 3
- 4
/ 5
- 6
\ 7 nodes loaded.
+5: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
+3: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
+6: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
 1: 
/ 1
- 2
\ 3 nodes loaded.
 1: ..:: Testing with homogeneous model ::..
-10: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
-10: Theta0 set to 0.134854
-10: Theta1 set to 0.00979053
-10: Theta2 set to 0.533357
-10: Theta3 set to 0.837934
-5: 
/ 1
- 2
\ 3
- 4
/ 5
- 6 nodes loaded.
 5: 4x4
 5: [
 5: [-1.37306, 0.362694, 0.906736, 0.103627]
@@ -1621,26 +1635,52 @@
 5: [0.259067, 0.362694, -0.777202, 0.15544]
 5: [0.0518135, 0.906736, 0.272021, -1.23057]
 5: ]
-10: Theta4 set to 0.983791
+10: Theta0 set to 0.478898
+10: Theta1 set to 0.208286
+10: Theta2 set to 0.491061
+10: Theta3 set to 0.854906
+10: Theta4 set to 0.842372
 10: Fast check:
- 1/13 Test  #8: test_nhx .........................   Passed    0.01 sec
+ 1/13 Test  #8: test_nhx .........................   Passed    0.04 sec
+test 11
+      Start 11: test_tree
+
+11: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree
+11: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
+11: Test timeout computed to be: 60000
 3: Testing Single Tree Traversal likelihood class...
 9: Initializing data structure............: Done.
 9: Number of distinct sites...............: 9
 9: Parsimony score: 9
 4: Initializing data structure............: Done.
 4: Number of distinct sites...............: 14
-3: Initializing data structure............: Done.
-3: Number of distinct sites...............: 12
 4: Test model.............................: T92
 4: 94.395699097704181213
 4: * initial likelihood...................: 94.3957
+3: Initializing data structure............: Done.
+3: Number of distinct sites...............: 12
+4: Log-likelihood after adding clock......: 94.3957
 3: Test model.............................: T92
 3: 85.030942031950203841
 3: * initial likelihood...................: 85.0309
-4: Log-likelihood after adding clock......: 94.3957
+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
+ 2/13 Test  #9: test_parsimony ...................   Passed    0.05 sec
+test 12
+      Start 12: test_tree_getpath
+
+12: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree_getpath
+12: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
+12: Test timeout computed to be: 60000
+3: Done.
+3: Tree scaled by.........................: 8.31477
+3: * likelihood after tree scale..........: 71.6905
 12: 
/ 1
- 2
\ 3
- 4
/ 5 nodes loaded.
- 2/13 Test  #9: test_parsimony ...................   Passed    0.01 sec
 12: Id node1 0
 12: Id node2 1
 12: Ids of path:
@@ -1655,18 +1695,14 @@
 12: 4
 12: 3
 12: 2
-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
- 3/13 Test #12: test_tree_getpath ................   Passed    0.01 sec
-13: Total length...........................: 100.754
+ 3/13 Test #12: test_tree_getpath ................   Passed    0.02 sec
+test 13
+      Start 13: test_tree_rootat
+
+13: Test command: /build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu/test/test_tree_rootat
+13: Working Directory: /build/reproducible-path/libbpp-phyl-2.4.1/test
+13: Test timeout computed to be: 60000
+13: Total length...........................: 102.361
 4: 
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
Optimizing... \ 23
Optimizing... - 24
Optimizing... / 25
Optimizing... - 26
Optimizing... \ 27
Optimizing... - 28
Optimizing... / 29
Optimizing... - 30
Optimizing... \ 31
Optimizing... - 32
 4: 
 4: 71.265799586318664183
@@ -1681,6 +1717,23 @@
 4: BrLen5	0.448312	[ 1e-06; 10000] 
 4: T92.kappa	0.996464	]0; +inf[
 4: T92.theta	0.579955	]1e-06; 0.999999[
+4: Initializing data structure............: Done.
+4: Number of distinct sites...............: 14
+4: Test model.............................: T92
+4: 92.32951163347922829416
+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: 71.26579406920922110658
+4: * likelihood after full optimization...: 71.2658
+4: Name:	Value:	Constraint:
+4: _________________________________________________
+4: TotalHeight	0.448127	[ 0; 10000] 
+4: HeightP4	0.390916	[ 0; 1] 
+4: HeightP2	0.819072	[ 0; 1] 
+4: T92.kappa	0.996398	]0; +inf[
+4: T92.theta	0.579960	]1e-06; 0.999999[
+ 4/13 Test  #4: test_likelihood_clock ............   Passed    0.12 sec
 3: 
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
Optimizing... \ 23
Optimizing... - 24
Optimizing... / 25
Optimizing... - 26
Optimizing... \ 27
Optimizing... - 28
Optimizing... / 29
Optimizing... - 30
Optimizing... \ 31
 3: 
 3: 65.72293577215084781074
@@ -1701,22 +1754,7 @@
 3: Done.
 3: Tree scaled by.........................: 8.31477
 3: * likelihood after tree scale..........: 71.6905
-4: Initializing data structure............: Done.
-4: Number of distinct sites...............: 14
-4: Test model.............................: T92
-4: 92.32951163347922829416
-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: 71.26579406920922110658
-4: * likelihood after full optimization...: 71.2658
-4: Name:	Value:	Constraint:
-4: _________________________________________________
-4: TotalHeight	0.448127	[ 0; 10000] 
-4: HeightP4	0.390916	[ 0; 1] 
-4: HeightP2	0.819072	[ 0; 1] 
-4: T92.kappa	0.996398	]0; +inf[
-4: T92.theta	0.579960	]1e-06; 0.999999[
+ 5/13 Test  #7: test_models ......................   Passed    0.20 sec
 3: 
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
Optimizing... \ 23
Optimizing... - 24
Optimizing... / 25
Optimizing... - 26
Optimizing... \ 27
Optimizing... - 28
Optimizing... / 29
Optimizing... - 30
Optimizing... \ 31
 3: 
 3: 65.72293577215017990056
@@ -1730,16 +1768,14 @@
 3: BrLen2	3.41183634498661625400	3.41183634498661714218
 3: BrLen3	-187.23500312397601419434	-187.23500312397607103776
 3: BrLen4	-56.02595035072955909072	-56.02595035072957330158
- 4/13 Test  #3: test_likelihood ..................   Passed    0.09 sec
- 5/13 Test  #4: test_likelihood_clock ............   Passed    0.09 sec
- 6/13 Test  #7: test_models ......................   Passed    0.10 sec
- 7/13 Test #13: test_tree_rootat .................   Passed    0.12 sec
+ 6/13 Test  #3: test_likelihood ..................   Passed    0.23 sec
+ 7/13 Test #13: test_tree_rootat .................   Passed    0.23 sec
 10: Initializing data structure............: Done.
-10: Number of distinct sites...............: 172
+10: Number of distinct sites...............: 186
 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...............: 70
-5: 76903.9
+5: Number of distinct sites...............: 77
+5: 77409.5
 5: Analytical (Laplace) total count:
 5: 4x4
 5: [
@@ -1769,47 +1805,6 @@
 5: [0, 0, 0, 0]
 5: ]
 5: Compute joint node-pairs likelihood....: 
-2: Br0 BrLen = 0.001 counts = 0.00082
-2: 4x4
-2: [
-2: [0, 0, 5e-05, 0]
-2: [6e-05, 0, 9e-05, 0.00016]
-2: [8e-05, 0.00015, 0, 4e-05]
-2: [0, 0.00016, 3e-05, 0]
-2: ]
-2: Br1 BrLen = 0.002 counts = 0.00226
-2: 4x4
-2: [
-2: [0, 0.0001, 0.00029, 2e-05]
-2: [0.00016, 0, 0.00032, 0.00036]
-2: [0.00017, 0.00024, 0, 9e-05]
-2: [2e-05, 0.00039, 0.0001, 0]
-2: ]
-2: Br2 BrLen = 0.003 counts = 0.00286
-2: 4x4
-2: [
-2: [0, 0.00014, 0.00024, 3e-05]
-2: [0.00013, 0, 0.00027, 0.00053]
-2: [0.00026, 0.00038, 0, 0.00014]
-2: [2e-05, 0.00049, 0.00023, 0]
-2: ]
-2: Br3 BrLen = 0.01 counts = 0.01031
-2: 4x4
-2: [
-2: [0, 0.00041, 0.00087, 0.00011]
-2: [0.00051, 0, 0.00129, 0.00193]
-2: [0.00079, 0.00125, 0, 0.00068]
-2: [0.00015, 0.00171, 0.00061, 0]
-2: ]
-2: Br4 BrLen = 0.1 counts = 0.10011
-2: 4x4
-2: [
-2: [0, 0.00384, 0.00887, 0.00113]
-2: [0.00334, 0, 0.01255, 0.01775]
-2: [0.00874, 0.01277, 0, 0.00555]
-2: [0.00107, 0.01872, 0.00578, 0]
-2: ]
- 8/13 Test  #2: test_detailed_simulations ........   Passed    0.79 sec
 5: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 5: Total count, decomposition method:
 5: 4x4
@@ -1849,6 +1844,47 @@
 5: [6.26538e-09, 0.000129478, 5.67996e-12, 5.21646e-08]
 5: [6.2614e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12]
 5: ]
+2: Br0 BrLen = 0.001 counts = 0.00095
+2: 4x4
+2: [
+2: [0, 4e-05, 6e-05, 1e-05]
+2: [5e-05, 0, 0.00014, 0.0002]
+2: [0.0001, 0.00012, 0, 4e-05]
+2: [2e-05, 0.00015, 2e-05, 0]
+2: ]
+2: Br1 BrLen = 0.002 counts = 0.00193
+2: 4x4
+2: [
+2: [0, 9e-05, 0.00012, 3e-05]
+2: [0.0001, 0, 0.00021, 0.00028]
+2: [0.00022, 0.00027, 0, 9e-05]
+2: [2e-05, 0.00037, 0.00013, 0]
+2: ]
+2: Br2 BrLen = 0.003 counts = 0.00328
+2: 4x4
+2: [
+2: [0, 0.00014, 0.00028, 6e-05]
+2: [0.00014, 0, 0.00038, 0.00052]
+2: [0.00029, 0.00053, 0, 0.00019]
+2: [3e-05, 0.00057, 0.00015, 0]
+2: ]
+2: Br3 BrLen = 0.01 counts = 0.00999
+2: 4x4
+2: [
+2: [0, 0.00042, 0.00093, 6e-05]
+2: [0.00032, 0, 0.00138, 0.00161]
+2: [0.00092, 0.00129, 0, 0.00066]
+2: [0.00014, 0.00183, 0.00043, 0]
+2: ]
+2: Br4 BrLen = 0.1 counts = 0.10219
+2: 4x4
+2: [
+2: [0, 0.004, 0.00955, 0.00128]
+2: [0.00343, 0, 0.01301, 0.01856]
+2: [0.00903, 0.01302, 0, 0.00556]
+2: [0.00097, 0.01796, 0.00582, 0]
+2: ]
+ 8/13 Test  #2: test_detailed_simulations ........   Passed    1.48 sec
 5: Compute joint node-pairs likelihood....: 
 5: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 5: checking saturation...
@@ -1924,9 +1960,15 @@
 5: [0.277113, 0.364216, 0.278181, 0.312009]
 5: ]
 5: 6.25012
-5: A	0.001	38	37.9655	37.9322	37.9322	37.9655	37.9655	37.9655	37.9655
-5: B	0.002	101	101.311	101.166	101.166	101.311	101.311	101.311	101.311
-5: 0.008	384	392.554	390.082	390.082	392.554	392.554	392.554	392.554
+5: A	0.001	45	45.7932	45.7581	45.7581	45.7932	45.7932	45.7932	45.7932
+5: B	0.002	106	105.548	105.392	105.392	105.548	105.548	105.548	105.548
+5: 0.008	407	404.787	402.181	402.181	404.787	404.787	404.787	404.787
+5: C	0.01	510	508.283	504.519	504.519	508.283	508.283	508.283	508.283
+5: D	0.02	1027	1026.71	1011.33	1011.33	1026.71	1026.71	1026.71	1026.71
+5: A	0.001	3.02192/3	3.02164/3	3.02164/3	6.02992/6	6.03382/6	6.03382/6	0.000554772/0	0.00127885/0	0.00127885/0	1.02792/1	1.02933/1	1.02933/1	
+5: B	0.002	3.0062/3	3.00966/3	3.00966/3	11.6969/12	11.7128/12	11.7128/12	0.0212965/0	0.0244078/0	0.0244078/0	4.00025/4	4.0042/4	4.0042/4	
+5: 0.008	18.2273/17	18.2889/17	18.2889/17	37.057/37	37.3723/37	37.3723/37	5.20158/5	5.18554/5	5.18554/5	19.5991/20	19.6671/20	19.6671/20	
+5: C	0.01	10.2307/10	10.392/10	10.392/10	45.5081/46	45.9025/46	45.9025/46	4.01885/4	4.01696/4	4.01696/4	11.9777/12	12.123/12	12.123/12	
 11: 
/ 1
- 2
\ 3
- 4
/ 5 nodes loaded.
 11: ((A:1,B:2):3,C:4);
 11: 
@@ -1955,15 +1997,11 @@
 11: Node 3:
 11: Node 4:
 11: B: ESS=2
-5: C	0.01	496	498.222	494.343	494.343	498.222	498.222	498.222	498.222
+5: D	0.02	40.9517/41	41.3136/41	41.3136/41	103.127/104	104.961/104	104.961/104	11.1463/10	11.0949/10	11.0949/10	35.266/36	35.67/36	35.67/36	
 11: Newick I/O ok.
-5: D	0.02	1000	996.886	981.608	981.608	996.886	996.886	996.886	996.886
-5: A	0.001	0.0059702/0	0.00712367/0	0.00712367/0	4.02686/4	4.02987/4	4.02987/4	0.00137333/0	0.0018151/0	0.0018151/0	1.98994/2	1.99043/2	1.99043/2	
-5: B	0.002	3.01201/3	3.01499/3	3.01499/3	10.1006/10	10.114/10	10.114/10	0.000108916/0	0.00230869/0	0.00230869/0	2.99607/3	3.00249/3	3.00249/3	
-5: 0.008	17.1102/17	17.1753/17	17.1753/17	39.3853/40	39.6732/40	39.6732/40	4.02065/4	4.01029/4	4.01029/4	14.4951/14	14.5576/14	14.5576/14	
-5: C	0.01	19.8839/21	19.9556/21	19.9556/21	42.89/42	43.3378/42	43.3378/42	2.20525/2	2.23296/2	2.23296/2	18.0361/18	18.2073/18	18.2073/18	
-5: D	0.02	31.6339/32	31.9983/32	31.9983/32	74.9595/78	76.658/78	76.658/78	6.03274/6	6.10318/6	6.10318/6	32.0325/32	32.633/32	32.633/32	
- 9/13 Test  #5: test_mapping .....................   Passed    1.38 sec
+ 9/13 Test  #5: test_mapping .....................   Passed    2.30 sec
+1: 
[                                      ]   0%
[>                                     ]   2%
[>>                                    ]   5%
[>>>                                   ]   7%
[>>>>                                  ]  10%
[>>>>>                                 ]  13%
[>>>>>>                                ]  15%
[>>>>>>>                               ]  18%
[>>>>>>>>                              ]  21%
[>>>>>>>>>                             ]  23%
[>>>>>>>>>>                            ]  26%
[>>>>>>>>>>>                           ]  29%
[>>>>>>>>>>>>                          ]  31%
[>>>>>>>>>>>>>                         ]  34%
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[>>>>>>>>>>>>>>>>>>>>>>>>>             ]  66%
[>>>>>>>>>>>>>>>>>>>>>>>>>>            ]  68%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>           ]  71%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  73%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         ]  76%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>        ]  79%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>       ]  81%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>      ]  84%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>     ]  87%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    ]  89%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>   ]  92%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>  ]  95%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ]  97%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0384	0.0056
+1: ..:: Testing with homogeneous, non-stationary model ::..
 11: Newick multiple I/O ok.
 11: Testing parsing a directory...
 11: Ok, reading on directory throws exception!
@@ -1993,23 +2031,13 @@
 11: 
/ 1
- 2
\ 3 nodes loaded.
 11: ((A:1):2);
 11: 
-10/13 Test #11: test_tree ........................   Passed    4.02 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%0.0385	0.0049
-1: ..:: Testing with homogeneous, non-stationary model ::..
-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%0.0388	0.0063
+10/13 Test #11: test_tree ........................   Passed    7.95 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%0.0409	0.0063
 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...............: 1004
-6: 96457.4
-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
-10: 
-10: 0.134854	0.131753
-10: 0.00979053	0.00849909
-10: 0.533357	0.531788
-10: 0.837934	0.828903
-10: 0.983791	0.984941
-10: Detailed check:
+6: Number of distinct sites...............: 976
+6: 96384.9
 6: Analytical total count:
 6: 64x64
 6: [
@@ -2079,10 +2107,18 @@
 6: [3.00168, 3.00159, 3.00152, 2.00023, 3.00171, 3.00178, 3.00167, 2.00023, 3.00146, 3.00169, 3.00179, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00169, 3.00174, 3.00152, 2.00023, 3.00163, 3.00169, 3.00172, 2.00023, 3.00149, 3.0016, 3.00175, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00169, 3.00167, 3.00146, 2.00023, 3.00171, 3.00171, 3.00166, 2.00023, 3.00149, 3.00165, 3.00177, 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...............: 178
-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%0.9362	0.801
+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
+10: 
+10: 0.478898	0.501136
+10: 0.208286	0.201305
+10: 0.491061	0.493898
+10: 0.854906	0.827836
+10: 0.842372	0.837814
+10: Detailed check:
+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%0.931	0.7972
 1: ..:: Testing with non-homogeneous, stationary model ::..
+10: Initializing data structure............: Done.
+10: Number of distinct sites...............: 183
 6: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 6: Simple total count:
 6: 64x64
@@ -2223,8 +2259,6 @@
 6: [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0]
 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%0.0383	0.0054
-11/13 Test  #1: test_bowker ......................   Passed   17.14 sec
 6: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
 6: Total count, uniformization method:
 6: 64x64
@@ -2366,24 +2400,26 @@
 6: ]
 6: Compute joint node-pairs likelihood....: 
 6: 
[                                      ]   0%
[>>>>>>>>>                             ]  25%
[>>>>>>>>>>>>>>>>>>>                   ]  50%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>          ]  75%
[>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done.
-12/13 Test  #6: test_mapping_codon ...............   Passed   18.52 sec
-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
+11/13 Test  #6: test_mapping_codon ...............   Passed   27.23 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%0.0374	0.0061
+12/13 Test  #1: test_bowker ......................   Passed   27.84 sec
+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
 10: 
-10: 0.134854	0.145807
-10: 0.00979053	0.0103918
-10: 0.533357	0.528051
-10: 0.837934	0.815193
-10: 0.983791	0.98361
-13/13 Test #10: test_simulations .................   Passed   21.55 sec
+10: 0.478898	0.480594
+10: 0.208286	0.212907
+10: 0.491061	0.471841
+10: 0.854906	0.85715
+10: 0.842372	0.843128
+13/13 Test #10: test_simulations .................   Passed   40.92 sec
 
 100% tests passed, 0 tests failed out of 13
 
-Total Test time (real) =  21.56 sec
+Total Test time (real) =  40.95 sec
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
    create-stamp debian/debhelper-build-stamp
    dh_prep
    dh_auto_install
-	cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+	cd obj-i686-linux-gnu && make -j10 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-i686-linux-gnu'
 /usr/bin/cmake -S/build/reproducible-path/libbpp-phyl-2.4.1 -B/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
 make  -f CMakeFiles/Makefile2 preinstall
@@ -2401,237 +2437,237 @@
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/i386-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/TreeTemplateTools.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/AncestralStateReconstruction.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/Io
--- 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/Nhx.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/IoFrequenciesSet.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/BppOMultiTreeWriterFormat.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/BppORateDistributionFormat.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/IoSubstitutionModel.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/IoDistanceMatrixFactory.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/Newick.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/BppOFrequenciesSetFormat.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/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/IoTree.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/Distance
--- 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/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/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/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/Model
--- 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/FrequenciesSet
--- 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/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/ProteinFrequenciesSet.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/FrequenciesSet/MvaFrequenciesSet.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/MixtureOfASubstitutionModel.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/SubstitutionModelSet.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/AbstractMixedSubstitutionModel.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/AbstractSubstitutionModel.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/MixtureOfSubstitutionModels.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/AbstractWordSubstitutionModel.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/AbstractKroneckerWordSubstitutionModel.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/FromMixtureSubstitutionModel.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/G2001.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/MarkovModulatedSubstitutionModel.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/AbstractBiblioMixedSubstitutionModel.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/MixedSubstitutionModel.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/Codon
+-- 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_M9.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/AbstractCodonFrequenciesSubstitutionModel.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/CodonDistanceSubstitutionModel.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/AbstractCodonFitnessSubstitutionModel.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/AbstractCodonBGCSubstitutionModel.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/AbstractCodonCpGSubstitutionModel.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/SENCA.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/YNGP_M1.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/Codon/KroneckerCodonDistanceFrequenciesSubstitutionModel.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/AbstractCodonDistanceSubstitutionModel.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/YN98.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/AbstractCodonSubstitutionModel.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/AbstractCodonAARateSubstitutionModel.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/AbstractCodonAAFitnessSubstitutionModel.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_M.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/CodonDistanceFrequenciesSubstitutionModel.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/CodonAdHocSubstitutionModel.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/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/YNGP_M3.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/KroneckerCodonDistanceSubstitutionModel.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/TripletSubstitutionModel.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/MG94.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/AbstractCodonFitnessSubstitutionModel.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/AbstractKroneckerCodonSubstitutionModel.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/GY94.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/AbstractCodonDistanceSubstitutionModel.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/OneChangeTransitionModel.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/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/MixtureOfASubstitutionModel.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/StateMap.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/Protein
 -- 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/LLG08_EX3.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/WAG01.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/LLG08_EHO.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/LLG08_UL3.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/DSO78.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/JTT92.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/ProteinSubstitutionModel.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/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_EX3.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/Coala.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/JCprot.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/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/LLG08_UL3.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/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/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/L95.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/gBGC.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/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/YpR.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/HKY85.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/F84.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/YpR.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/Nucleotide/JCnuc.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/L95.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/NucleotideSubstitutionModel.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/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/CodonFrequenciesSet.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/FrequenciesSet.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/FrequenciesSet/ProteinFrequenciesSet.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/InMixedSubstitutionModel.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/G2001.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/RateDistribution
 -- 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/ExponentialDiscreteRateDistribution.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/RateDistribution/ConstantRateDistribution.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/MixedSubstitutionModelSet.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/RE08.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/OneChangeTransitionModel.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/NNITopologySearch.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/InMixedSubstitutionModel.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/Io
+-- 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/BppOTransitionModelFormat.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/BppOMultiTreeWriterFormat.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/IoTree.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/PhylipDistanceMatrixFormat.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/BppOSubstitutionModelFormat.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/Newick.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/BppOMultiTreeReaderFormat.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/BppOTreeWriterFormat.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/IoDistanceMatrixFactory.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/SitePatterns.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/BipartitionTools.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/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/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/NaiveSubstitutionCount.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/ProbabilisticSubstitutionMapping.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/Mapping.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/DecompositionMethods.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/DecompositionSubstitutionCount.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/SubstitutionMapping.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/NaiveSubstitutionCount.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/CategorySubstitutionRegister.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/SubstitutionMappingTools.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/ProbabilisticRewardMapping.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/SubstitutionMappingTools.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/UniformizationSubstitutionCount.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/TreeTemplateTools.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/NNITopologySearch.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/TreeTemplate.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/Parsimony
--- 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/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/Parsimony/TreeParsimonyData.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/DRTreeParsimonyScore.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/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/NNISearchable.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/TreeDrawingListener.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/TreeDrawing.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/Graphics/TreeDrawing.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/Tree.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/PhyloStatistics.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/SitePatterns.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/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/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/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/NonHomogeneousSequenceSimulator.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/TreeExceptions.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/TreeDrawingListener.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/PGMA.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/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/DistanceMethod.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/NeighborJoining.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/Likelihood
+-- 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/RNonHomogeneousTreeLikelihood.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/MarginalAncestralStateReconstruction.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/RNonHomogeneousMixedTreeLikelihood.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/TreeLikelihoodTools.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/GlobalClockTreeLikelihoodFunctionWrapper.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/RNonHomogeneousTreeLikelihood.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/AbstractNonHomogeneousTreeLikelihood.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/RHomogeneousClockTreeLikelihood.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/DRHomogeneousTreeLikelihood.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/NonHomogeneousTreeLikelihood.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/AbstractTreeLikelihoodData.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/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/RASTools.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/DRASRTreeLikelihoodData.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/DRNonHomogeneousTreeLikelihood.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/TreeLikelihood.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/AbstractTreeLikelihoodData.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/DRTreeLikelihoodTools.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/DRHomogeneousMixedTreeLikelihood.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/HomogeneousTreeLikelihood.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/NNIHomogeneousTreeLikelihood.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/TopologySearch.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/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/DRTreeLikelihood.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/ClockTreeLikelihood.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/TreeLikelihoodTools.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/Tree.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/NodeTemplate.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/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/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/DetailedSiteSimulator.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/SiteSimulator.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/lib/i386-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets.cmake
 -- Installing: /build/reproducible-path/libbpp-phyl-2.4.1/debian/tmp/usr/lib/i386-linux-gnu/cmake/bpp-phyl/bpp-phyl-targets-none.cmake
 make[1]: Leaving directory '/build/reproducible-path/libbpp-phyl-2.4.1/obj-i686-linux-gnu'
@@ -2680,9 +2716,9 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-10_i386.deb'.
-dpkg-deb: building package 'libbpp-phyl12t64' in '../libbpp-phyl12t64_2.4.1-10_i386.deb'.
 dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-10_i386.deb'.
+dpkg-deb: building package 'libbpp-phyl12t64' in '../libbpp-phyl12t64_2.4.1-10_i386.deb'.
+dpkg-deb: building package 'libbpp-phyl12t64-dbgsym' in '../libbpp-phyl12t64-dbgsym_2.4.1-10_i386.deb'.
  dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-10_i386.buildinfo
  dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-10_i386.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -2690,12 +2726,14 @@
 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/61881/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/61881/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/41215 and its subdirectories
-I: Current time: Sun Jun  8 05:51:09 -12 2025
-I: pbuilder-time-stamp: 1749405069
+I: removing directory /srv/workspace/pbuilder/61881 and its subdirectories
+I: Current time: Tue May  7 01:35:47 +14 2024
+I: pbuilder-time-stamp: 1714995347