Diff of the two buildlogs: -- --- b1/build.log 2025-11-20 08:23:11.286461614 +0000 +++ b2/build.log 2025-11-20 08:25:24.370607550 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Nov 19 20:20:58 -12 2025 -I: pbuilder-time-stamp: 1763626858 +I: Current time: Thu Dec 24 04:46:13 +14 2026 +I: pbuilder-time-stamp: 1798037173 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -33,53 +33,85 @@ dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3662945/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2010628/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Dec 23 14:46 /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/2010628/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2010628/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='arm64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 nocheck' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f1a1d5f726874e909c9d3c0ca5b3c5cd' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='3662945' - PS1='# ' - PS2='> ' + INVOCATION_ID=1bc13348e94c4ddab4b6eaafb2dafd35 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2010628 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.KkrdKMmm/pbuilderrc_QshK --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KkrdKMmm/b1 --logfile b1/build.log prime-phylo_1.0.11-14.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.KkrdKMmm/pbuilderrc_4TB1 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.KkrdKMmm/b2 --logfile b2/build.log prime-phylo_1.0.11-14.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.57+deb13-cloud-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3662945/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2010628/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -285,7 +317,7 @@ Get: 142 http://deb.debian.org/debian forky/main arm64 liblapack-dev arm64 3.12.1-7 [3829 kB] Get: 143 http://deb.debian.org/debian forky/main arm64 liblzma-dev arm64 5.8.1-2 [344 kB] Get: 144 http://deb.debian.org/debian forky/main arm64 libxml2-dev arm64 2.15.1+dfsg-0.4 [720 kB] -Fetched 130 MB in 1s (181 MB/s) +Fetched 130 MB in 1s (194 MB/s) Preconfiguring packages ... Selecting previously unselected package m4. (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 ... 19964 files and directories currently installed.) @@ -893,7 +925,11 @@ Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/reproducible-path/prime-phylo-1.0.11/ && 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 > ../prime-phylo_1.0.11-14_source.changes +I: user script /srv/workspace/pbuilder/2010628/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/2010628/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/prime-phylo-1.0.11/ && 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 > ../prime-phylo_1.0.11-14_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-14 dpkg-buildpackage: info: source distribution unstable @@ -917,7 +953,7 @@ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo \ -DCMAKE_BUILD_TYPE=RELEASE - cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. + cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu -DBUILD_TESTING:BOOL=OFF -Dofficial_binary_packaging=on -Dprime_dynamic=on -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_INSTALL_RPATH=/usr/lib/prime-phylo -DCMAKE_BUILD_TYPE=RELEASE .. -- The CXX compiler identification is GNU 15.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done @@ -965,7 +1001,7 @@ -- Found LibXml2: /usr/lib/aarch64-linux-gnu/libxml2.so (found version "2.15.1") mpilib is /usr/lib/aarch64-linux-gnu/openmpi/include;/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi included path is --- Configuring done (7.1s) +-- Configuring done (7.4s) CMake Warning (dev) at src/cxx/tools/tree2leafnames/CMakeLists.txt:4 (add_executable): Policy CMP0115 is not set: Source file extensions must be explicit. Run "cmake --help-policy CMP0115" for policy details. Use the cmake_policy @@ -980,6 +1016,7 @@ CMake Warning: Manually-specified variables were not used by the project: + BUILD_TESTING CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR @@ -1000,10 +1037,10 @@ make[2]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 0%] [BISON][MyParser2] Building parser with bison 3.8.2 -cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y [ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/flex -o/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l +[ 1%] [BISON][MyParser2] Building parser with bison 3.8.2 +cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile && /usr/bin/bison -d -d -o /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c gb.y gb.y: warning: 1 nonterminal useless in grammar [-Wother] gb.y: warning: 1 rule useless in grammar [-Wother] gb.y:259.1-12: warning: nonterminal useless in grammar: darwin_entry [-Wother] @@ -1013,14 +1050,14 @@ make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 1%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -MF CMakeFiles/prime-phylo-sfile.dir/sfile.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gbread.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c +[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o +[ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -MF CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -MF CMakeFiles/prime-phylo-sfile.dir/lexer.c.o.d -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_new_sequence': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:35:1: warning: old-style function definition [-Wold-style-definition] 35 | seq_new_sequence(locus, type, definition, length) @@ -1088,9 +1125,9 @@ [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 5%] [BISON][MyParser] Building parser with bison 3.8.2 [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l +[ 5%] [BISON][MyParser] Building parser with bison 3.8.2 cd /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 108 | %expect 4 @@ -1099,29 +1136,29 @@ make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 5%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -MF CMakeFiles/prime-phylo.dir/NHXnode.c.o.d -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c -[ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -MF CMakeFiles/prime-phylo.dir/NHXtree.c.o.d -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c +[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o cd 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-Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -MF CMakeFiles/prime-phylo.dir/NHXannotation.c.o.d -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE 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/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard 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-DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -MF CMakeFiles/prime-phylo.dir/lexer.c.o.d -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c +[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -MF CMakeFiles/prime-phylo.dir/AnError.cc.o.d -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc +[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o +[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o -MF CMakeFiles/prime-phylo.dir/BeepOption.cc.o.d -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o -MF CMakeFiles/prime-phylo.dir/Hacks.cc.o.d -o CMakeFiles/prime-phylo.dir/Hacks.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Hacks.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.cc.o -MF CMakeFiles/prime-phylo.dir/ODESolver.cc.o.d -o CMakeFiles/prime-phylo.dir/ODESolver.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PRNG.cc.o -MF CMakeFiles/prime-phylo.dir/PRNG.cc.o.d -o CMakeFiles/prime-phylo.dir/PRNG.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PRNG.cc -[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -MF CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o.d -o CMakeFiles/prime-phylo.dir/PrimeOptionMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc NHXparse.y: In function 'read_tree_string': NHXparse.y:402:20: warning: passing argument 1 of 'read_from_string' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] @@ -1133,6 +1170,8 @@ | | | | int double | %f +[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c:1597:16: warning: 'input' defined but not used [-Wunused-function] 1597 | static int input (void) | ^~~~~ @@ -1143,18 +1182,22 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c:80:3: warning: '__builtin_strncpy' specified bound 5 equals destination size [-Wstringop-truncation] 80 | strncpy(a->anno_type, tag, MAX_ANNOTATION_ID_LENGTH); | ^ -[ 12%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -MF CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ProbabilityModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ProbabilityModel.cc [ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -MF CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc [ 14%] 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o -MF CMakeFiles/prime-phylo.dir/Probability.cc.o.d -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -MF CMakeFiles/prime-phylo.dir/Tokenizer.cc.o.d -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc: In member function 'std::pair beep::option::BeepOptionMap::getDoubleX2(std::string)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:592:59: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 592 | pair BeepOptionMap::getDoubleX2(string name) - | ^ +[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + 405 | catch(std::exception e) + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] + 423 | catch(std::exception e) + | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; @@ -1264,19 +1307,13 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -[ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -MF CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o.d -o CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TimeEstimator.cc +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc: In member function 'std::pair beep::option::BeepOptionMap::getDoubleX2(std::string)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc:592:59: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 592 | pair BeepOptionMap::getDoubleX2(string name) + | ^ [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/BranchSwapping.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.cc [ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - 405 | catch(std::exception e) - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:30: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] - 423 | catch(std::exception e) - | ^ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/DiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscTree.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscTree.cc [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscPtMaps.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc @@ -1296,32 +1333,6 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc [ 21%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -MF CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o.d -o CMakeFiles/prime-phylo.dir/NodeNodeMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc:3: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMaps.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator @@ -1354,16 +1365,42 @@ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.cc:3: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc +[ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -MF CMakeFiles/prime-phylo.dir/StrStrMap.cc.o.d -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StrStrMap.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o -MF CMakeFiles/prime-phylo.dir/Tree.cc.o.d -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -MF CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o.d -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o @@ -1403,6 +1440,10 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -MF CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o.d -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc +[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc +[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, @@ -1448,12 +1489,12 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ -[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_common.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc -[ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -MF CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2PMCMC.cc +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] + 118 | buf[ bytes_read ]=NULL; + | ^~~~ [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC.cc [ 31%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o @@ -1462,10 +1503,6 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateModel_common.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateModel_common.cc [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:29: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] - 118 | buf[ bytes_read ]=NULL; - | ^~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc:5: @@ -1499,32 +1536,23 @@ | ^~~~~~~~ [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -MF CMakeFiles/prime-phylo.dir/GammaDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc +[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -MF CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc +[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc +[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -MF CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function 'void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable 'fparam' [-Wunused-variable] 104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime); | ^~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable] + 105 | Real rparam = variance * (rtime + ltime); + | ^~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 106 | for (int i = 0; i < t.size(); i++) | ~~^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:105:30: warning: unused variable 'rparam' [-Wunused-variable] - 105 | Real rparam = variance * (rtime + ltime); - | ^~~~~~ -[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -MF CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc -[ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] - 76 | virtual void init(EdgeWeightModel& erm); - | ^~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' - 140 | virtual void init(EdgeRateModel& erm); - | ^~~~ -[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -MF CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc -[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -MF CMakeFiles/prime-phylo.dir/NormalDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.cc:1: @@ -1534,16 +1562,23 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] + 76 | virtual void init(EdgeWeightModel& erm); + | ^~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' + 140 | virtual void init(EdgeRateModel& erm); + | ^~~~ +[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -MF CMakeFiles/prime-phylo.dir/NormalDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -MF CMakeFiles/prime-phylo.dir/UniformDensity.cc.o.d -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/VarRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc -[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -MF CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -MF CMakeFiles/prime-phylo.dir/VarRateModel.cc.o.d -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] @@ -1552,25 +1587,16 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:55:17: note: by 'virtual beep::Probability beep::InvGaussDensity::operator()(const beep::Real&) const' 55 | Probability operator()(const Real& x) const; | ^~~~~~~~ -[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -MF CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc +[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc [ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/MCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MCMCModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCModel.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' - 54 | Probability operator()(const Real& x) const; - | ^~~~~~~~ [ 39%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -MF CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o.d -o CMakeFiles/prime-phylo.dir/StdMCMCModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MCMCObject.cc.o @@ -1579,8 +1605,6 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc [ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc -[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleML.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] @@ -1589,20 +1613,25 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ -[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' + 54 | Probability operator()(const Real& x) const; + | ^~~~~~~~ +[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleML.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/GSRSampler.cc -[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc -[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc -[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc +[ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1626,21 +1655,29 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ -[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && 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src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc -[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc +[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/GSRSampler.cc +[ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -MF CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/PosteriorSampler.cc +[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -MF CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o.d -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc +[ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable] 78 | unsigned check_number_nonupdate = 0; | ^~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc +[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -MF CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc +[ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc @@ -1714,38 +1751,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by 'beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)' 23 | class BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 31 | class EdgeDiscPtMapIterator : public std::iterator - | ^~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:65, - from /usr/include/c++/15/bits/specfun.h:43, - from /usr/include/c++/15/cmath:3913, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 42 | std::iterator(), - | ^~~~~~~~ -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 54 | std::iterator(), - | ^~~~~~~~ -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 64 | std::iterator(), - | ^~~~~~~~ -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o @@ -1754,25 +1759,14 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -MF CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -MF CMakeFiles/prime-phylo.dir/GammaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc -[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' - 55 | Probability operator()(const Real& x) const; - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 31 | class EdgeDiscPtMapIterator : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/15/bits/stl_algobase.h:65, - from /usr/include/c++/15/vector:64, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: + from /usr/include/c++/15/bits/specfun.h:43, + from /usr/include/c++/15/cmath:3913, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ @@ -1797,38 +1791,12 @@ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder] - 588 | bool m_calculatedAtAndBelow; - | ^~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder] - 583 | bool m_calculatedAtBars; - | ^~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] - 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, - | ^~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable] - 485 | Point xpt = x.getPt(); - | ^~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable] - 528 | Node *parent = u->getParent(); - | ^~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] - 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); - | ^~~~~~~~ +[ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc [ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumerateReconciliationModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ @@ -1937,10 +1905,9 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc:3: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] 359 | static const Real C2 = 1.0 / 5.0; | ^~ @@ -2049,10 +2016,76 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ -[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc -[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc +[ 54%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' + 55 | Probability operator()(const Real& x) const; + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 31 | class EdgeDiscPtMapIterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:65, + from /usr/include/c++/15/vector:64, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:1: +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 42 | std::iterator(), + | ^~~~~~~~ +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 54 | std::iterator(), + | ^~~~~~~~ +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In copy constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(const beep::EdgeDiscPtMapIterator&)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:64:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 64 | std::iterator(), + | ^~~~~~~~ +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder] + 588 | bool m_calculatedAtAndBelow; + | ^~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:583:14: warning: 'bool beep::EdgeDiscGSR::m_calculatedAtBars' [-Wreorder] + 583 | bool m_calculatedAtBars; + | ^~~~~~~~~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:23:5: warning: when initialized here [-Wreorder] + 23 | EdgeDiscGSR::EdgeDiscGSR(Tree* G, + | ^~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'void beep::EdgeDiscGSR::convertDensitiesToProbabilities()': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:475:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 475 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:485:27: warning: variable 'xpt' set but not used [-Wunused-but-set-variable] + 485 | Point xpt = x.getPt(); + | ^~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:525:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 525 | for (int i = 0; i < m_G->getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:528:19: warning: unused variable 'parent' [-Wunused-variable] + 528 | Node *parent = u->getParent(); + | ^~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc: In member function 'beep::Probability beep::EdgeDiscGSR::getTotalPlacementDensity(const beep::Node*)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] + 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); + | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; @@ -2063,6 +2096,8 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ +[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM_BirthDeathProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:359:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::ODESolver::C2' of non-integral type [-fpermissive] @@ -2177,25 +2212,28 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] 50 | static const Real REL_TOL = 1e-6; | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ +[ 55%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/fastGEM.cc.o -MF CMakeFiles/prime-phylo.dir/fastGEM.cc.o.d -o CMakeFiles/prime-phylo.dir/fastGEM.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc:5: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -2216,6 +2254,12 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:60:18: warning: 'virtual void beep::ReconciliationModel::setGamma(const beep::GammaMap&)' was hidden [-Woverloaded-virtual=] + 60 | virtual void setGamma(const GammaMap& newGamma); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:188:10: note: by 'void beep::EnumerateLabeledReconciliationModel::setGamma(unsigned int)' + 188 | void setGamma(unsigned unique); + | ^~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -MF CMakeFiles/prime-phylo.dir/LambdaMap.cc.o.d -o CMakeFiles/prime-phylo.dir/LambdaMap.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, @@ -2258,9 +2302,8 @@ 18 | class fastGEM_BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -2281,22 +2324,10 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:60:18: warning: 'virtual void beep::ReconciliationModel::setGamma(const beep::GammaMap&)' was hidden [-Woverloaded-virtual=] - 60 | virtual void setGamma(const GammaMap& newGamma); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumerateReconciliationModel.hh:188:10: note: by 'void beep::EnumerateLabeledReconciliationModel::setGamma(unsigned int)' - 188 | void setGamma(unsigned unique); - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] - 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:17:9: note: by 'beep::fastGEM_BirthDeathProbs& beep::fastGEM_BirthDeathProbs::operator=(const beep::fastGEM_BirthDeathProbs&)' - 17 | class fastGEM_BirthDeathProbs : public BirthDeathProbs - | ^~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc +[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -MF CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o.d -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:2: @@ -2327,8 +2358,6 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -MF CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o.d -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:21: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); @@ -2349,10 +2378,16 @@ cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc [ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.cc:5: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] + 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathProbs.hh:17:9: note: by 'beep::fastGEM_BirthDeathProbs& beep::fastGEM_BirthDeathProbs::operator=(const beep::fastGEM_BirthDeathProbs&)' + 17 | class fastGEM_BirthDeathProbs : public BirthDeathProbs + | ^~~~~~~~~~~~~~~~~~~~~~~ [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc -[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.hh:6, @@ -2377,17 +2412,15 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc [ 60%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc -[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc -[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -2408,13 +2441,19 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc +[ 61%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc +[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc +[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -MF CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o.d -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc +[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 29 | NodeMap(const Tree &G); @@ -2432,6 +2471,7 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.hh:5, @@ -2456,43 +2496,12 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc:5: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -MF CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o.d -o CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -MF CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o.d -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc -[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:6: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -2513,68 +2522,14 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] - 161 | Probability p = calculateDataProbability(); - | ^ +[ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -MF CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o.d -o CMakeFiles/prime-phylo.dir/SetOfNodes.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SetOfNodes.cc +[ 64%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/TopTimeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TopTimeMCMC.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBranchSwapping.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTree.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc -[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.hh:12, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.hh:16, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:4: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] - 319 | typedef std::map::const_iterator MapIter; - | ^~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBranchSwapping.cc:3: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] @@ -2613,19 +2568,44 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.hh:12, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeMCMC.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] @@ -2654,66 +2634,18 @@ | ^~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -MF CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' + 55 | Probability operator()(const Real& x) const; + | ^~~~~~~~ [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] - 64 | virtual TreeIO& operator=(const TreeIO &io); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' - 39 | HybridTreeIO& operator=(const HybridTreeIO& io); - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] - 58 | virtual Tree& operator=(const Tree& T); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' - 24 | HybridTree& operator=(const HybridTree& T); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] - 269 | virtual Real imbalance(); - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' - 94 | Real imbalance() const; - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] - 316 | virtual Real imbalance(Node *v); - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' - 94 | Real imbalance() const; - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' - 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' - 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, - | ^~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.hh:16, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:6: @@ -2741,43 +2673,71 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self] 31 | ReconciliationTreeGenerator:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:20, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.cc:8: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' - 55 | Probability operator()(const Real& x) const; - | ^~~~~~~~ -[ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc -[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] - 367 | if(rootNode && bTree.getRootNode() == false) - | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:4: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:6: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.hh:16, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:4: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc: In member function 'std::string beep::ReconciliationTimeModel::table4os() const': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeModel.cc:319:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] + 319 | typedef std::map::const_iterator MapIter; + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] + 161 | Probability p = calculateDataProbability(); + | ^ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ @@ -2790,6 +2750,12 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] 269 | virtual Real imbalance(); | ^~~~~~~~~ @@ -2814,10 +2780,14 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc -[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] + 64 | virtual TreeIO& operator=(const TreeIO &io); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' + 39 | HybridTreeIO& operator=(const HybridTreeIO& io); + | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DLRSOrthoCalculator.hh:22: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] @@ -2856,35 +2826,41 @@ /usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here 129 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc +[ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] + 367 | if(rootNode && bTree.getRootNode() == false) + | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ +[ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc +[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeGenerator.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, @@ -2913,35 +2889,19 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] - 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' - 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:58:19: warning: 'virtual beep::Tree& beep::BirthDeathProbs::getStree() const' was hidden [-Woverloaded-virtual=] - 58 | virtual Tree& getStree() const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by 'beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()' - 40 | HybridTree& getStree(); - | ^~~~~~~~ +[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ @@ -2954,43 +2914,53 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] - 316 | virtual Real imbalance(Node *v); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] + 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] - 269 | virtual Real imbalance(); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] + 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:4: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeGenerator.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc:5: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDHybridTreeGenerator.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, @@ -3001,8 +2971,8 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, @@ -3019,18 +2989,20 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +[ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc [ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/HybridHostTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, @@ -3057,8 +3029,7 @@ | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); | ^~~~~~~~ @@ -3071,18 +3042,14 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by 'beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()' 40 | HybridTree& getStree(); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' was hidden [-Woverloaded-virtual=] - 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:22:9: note: by 'beep::BirthDeathInHybridMCMC& beep::BirthDeathInHybridMCMC::operator=(const beep::BirthDeathInHybridMCMC&)' - 22 | class BirthDeathInHybridMCMC : public StdMCMCModel, - | ^~~~~~~~~~~~~~~~~~~~~~ +[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ @@ -3116,20 +3083,20 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -[ 71%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc +[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BDTreeGenerator.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.hh:4, @@ -3183,54 +3150,52 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:5: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 72%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -MF CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o.d -o CMakeFiles/prime-phylo.dir/EnumHybridGuestTreeModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc +[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:8, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] + 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: note: by 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' + 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:58:19: warning: 'virtual beep::Tree& beep::BirthDeathProbs::getStree() const' was hidden [-Woverloaded-virtual=] + 58 | virtual Tree& getStree() const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:40:17: note: by 'beep::HybridTree& beep::BirthDeathInHybridProbs::getStree()' + 40 | HybridTree& getStree(); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.hh:33:38: warning: 'virtual beep::BirthDeathInHybridProbs& beep::BirthDeathInHybridProbs::operator=(const beep::BirthDeathInHybridProbs&)' was hidden [-Woverloaded-virtual=] + 33 | virtual BirthDeathInHybridProbs& operator=(const BirthDeathInHybridProbs& dsp); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.hh:22:9: note: by 'beep::BirthDeathInHybridMCMC& beep::BirthDeathInHybridMCMC::operator=(const beep::BirthDeathInHybridMCMC&)' + 22 | class BirthDeathInHybridMCMC : public StdMCMCModel, + | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc:6: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, @@ -3247,21 +3212,22 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ @@ -3310,14 +3276,17 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] - 64 | virtual TreeIO& operator=(const TreeIO &io); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' - 39 | HybridTreeIO& operator=(const HybridTreeIO& io); - | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' + 54 | Probability operator()(const Real& x) const; + | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeNodeMap.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] @@ -3369,21 +3338,35 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/CacheSubstitutionModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc -[ 73%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/FastCacheSubstitutionModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc -[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixCache.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc -[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc -[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:4: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:5: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:9, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeModel.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ @@ -3417,79 +3400,96 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' + 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, + | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] + 58 | virtual Tree& operator=(const Tree& T); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' + 24 | HybridTree& operator=(const HybridTree& T); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] + 269 | virtual Real imbalance(); + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' + 94 | Real imbalance() const; + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] + 316 | virtual Real imbalance(Node *v); + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' + 94 | Real imbalance() const; + | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeModel.cc:6: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:4: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:54:17: note: by 'virtual beep::Probability beep::NormalDensity::operator()(const beep::Real&) const' - 54 | Probability operator()(const Real& x) const; - | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' + 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, + | ^~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridHostTreeMCMC.cc:6: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] + 64 | virtual TreeIO& operator=(const TreeIO &io); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' + 39 | HybridTreeIO& operator=(const HybridTreeIO& io); + | ^~~~~~~~ +[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixCache.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixCache.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.cc In file included from /usr/include/c++/15/ext/hash_map:60, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:8, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:1: /usr/include/c++/15/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ +[ 74%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/TransitionHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc +[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -MF CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o.d -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o -MF CMakeFiles/prime-phylo.dir/SeqIO.cc.o.d -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:8: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | MatrixCache(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 32 | MatrixCache(const MatrixCache &C); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' [ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceType.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); @@ -3511,17 +3511,6 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] - 76 | virtual void init(EdgeWeightModel& erm); - | ^~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' - 140 | virtual void init(EdgeRateModel& erm); - | ^~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, @@ -3563,18 +3552,54 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EnumHybridGuestTreeMCMC.cc:1: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:4: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] + 76 | virtual void init(EdgeWeightModel& erm); + | ^~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' + 140 | virtual void init(EdgeRateModel& erm); + | ^~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LambdaMap.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.hh:4, @@ -3586,20 +3611,20 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, @@ -3628,8 +3653,16 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceData.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc:8: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | MatrixCache(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 32 | MatrixCache(const MatrixCache &C); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:5: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.hh:131:17: warning: 'virtual std::string beep::SubstitutionModel::print() const' was hidden [-Woverloaded-virtual=] 131 | std::string print() const; @@ -3648,6 +3681,10 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ +[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceType.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc +[ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o -MF CMakeFiles/prime-phylo.dir/SequenceData.cc.o.d -o CMakeFiles/prime-phylo.dir/SequenceData.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TransitionHandler.cc:2: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:31:23: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] @@ -3660,10 +3697,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc -[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc -[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Vector.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] @@ -3686,17 +3719,14 @@ 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' +[ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc +[ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Vector.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_Matrix.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc [ 80%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -MF CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o.d -o CMakeFiles/prime-phylo.dir/LA_DiagonalMatrix.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_DiagonalMatrix.cc -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const SequenceType&)' has not been declared within 'beep' - 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) - | ^~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend' - 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); - | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:19:5: warning: 'beep::LA_Matrix::dim' is initialized with itself [-Winit-self] 19 | LA_Matrix::LA_Matrix() @@ -3705,6 +3735,20 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Matrix.cc:20:13: warning: '*this.beep::LA_Matrix::dim' is used uninitialized [-Wuninitialized] 20 | : dim(dim), | ^~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const SequenceType&)' has not been declared within 'beep' + 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) + | ^~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:8: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend' + 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 288 | for (int i = 0; i < seqType.alphabetSize(); i++) + | ~~^~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] + 303 | for (int j = 0; j < seq.length(); j++) { + | ~~^~~~~~~~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] 76 | virtual void init(EdgeWeightModel& erm); @@ -3716,13 +3760,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 288 | for (int i = 0; i < seqType.alphabetSize(); i++) - | ~~^~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:303:35: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string::size_type' {aka 'long unsigned int'} [-Wsign-compare] - 303 | for (int j = 0; j < seq.length(); j++) { - | ~~^~~~~~~~~~~~~~ [ 81%] Linking CXX shared library libprime-phylo.so cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cmake -E cmake_link_script CMakeFiles/prime-phylo.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,--dependency-file=CMakeFiles/prime-phylo.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libprime-phylo.so -o libprime-phylo.so 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"CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o" "CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o" "CMakeFiles/prime-phylo.dir/mcmc/PosteriorSampler.cc.o" "CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o" "CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o" "CMakeFiles/prime-phylo.dir/MultiGSR.cc.o" "CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o" "CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o" "CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o" "CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o" "CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o" "CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o" "CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o" "CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o" "CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o" "C/usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0: warning: GCS is required by -z gcs, but this shared library lacks the necessary property note. The dynamic loader might not enable GCS or refuse to load the program unless all the shared library dependencies have the GCS marking. @@ -3737,108 +3774,100 @@ [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend -make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend -make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend -make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend -make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 83%] Generating cmdline.c, cmdline.h [ 82%] Generating cmdline.c, cmdline.h +make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM +make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend +make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 84%] Generating cmdline.c, cmdline.h make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 82%] Generating cmdline.c, cmdline.h +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" +[ 83%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h -[ 84%] Generating cmdline.c, cmdline.h -[ 85%] Generating cmdline.c, cmdline.h cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile [ 85%] Generating cmdline.c, cmdline.h -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot +[ 85%] Generating cmdline.c, cmdline.h +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 85%] Generating cmdline.c, cmdline.h +make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build +make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake "--color=" [ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -MF CMakeFiles/primeDTLSR.dir/idolatrous.cc.o.d -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build +[ 85%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" [ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -MF CMakeFiles/primeDLRS.dir/primeDLRS.cc.o.d -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/prime-phylo-1.0.11 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake "--color=" +cd 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/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong 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'/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build -make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make 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/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -MF CMakeFiles/reconcile.dir/reconcile.cc.o.d -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.c make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build +make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime 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-fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -MF CMakeFiles/primeGEM.dir/cmdline.c.o.d -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:3: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] - 64 | virtual TreeIO& operator=(const TreeIO &io); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' - 39 | HybridTreeIO& operator=(const HybridTreeIO& io); - | ^~~~~~~~ -[ 92%] Building C object src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/showtree/CMakeFiles/showtree.dir/cmdline.c.o -MF CMakeFiles/showtree.dir/cmdline.c.o.d -o CMakeFiles/showtree.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.c +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o -MF CMakeFiles/reroot.dir/reroot.cc.o.d -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc +[ 90%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -MF CMakeFiles/reconcile.dir/reconcile.cc.o.d -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc +[ 91%] Building C object src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/treesize/CMakeFiles/treesize.dir/cmdline.c.o -MF CMakeFiles/treesize.dir/cmdline.c.o.d -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.c In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:8: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] @@ -3877,25 +3906,37 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ +[ 92%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc: In function 'int main(int, char**)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:55:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] 55 | switch(args_info.input_format_arg) | ^ +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc:90:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 90 | catch (AnError e) { | ^ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:3: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIO.hh:64:21: warning: 'virtual beep::TreeIO& beep::TreeIO::operator=(const beep::TreeIO&)' was hidden [-Woverloaded-virtual=] + 64 | virtual TreeIO& operator=(const TreeIO &io); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.hh:39:19: note: by 'beep::HybridTreeIO& beep::HybridTreeIO::operator=(const beep::HybridTreeIO&)' + 39 | HybridTreeIO& operator=(const HybridTreeIO& io); + | ^~~~~~~~ +[ 93%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -MF CMakeFiles/reroot.dir/cmdline.c.o.d -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.c In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:4: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] @@ -3904,32 +3945,32 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] - 316 | virtual Real imbalance(Node *v); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] + 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] - 269 | virtual Real imbalance(); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] + 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; @@ -3957,8 +3998,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:198:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 198 | catch (AnError e) | ^ -[ 92%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -MF CMakeFiles/chainsaw.dir/cmdline.c.o.d -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:7: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] 58 | virtual Tree& operator=(const Tree& T); @@ -3967,12 +4006,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] 333 | virtual std::string subtree4os(Node* v, int indent) const; | ^~~~~~~~~~ @@ -3985,26 +4018,32 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' 108 | std::string subtree4os(Node *v, std::string indent_left, | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] - 316 | virtual Real imbalance(Node *v); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] + 269 | virtual Real imbalance(); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] - 269 | virtual Real imbalance(); +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] + 316 | virtual Real imbalance(Node *v); | ^~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' 94 | Real imbalance() const; | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, | ^~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, @@ -4016,44 +4055,17 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:95:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 95 | catch (AnError e) { | ^ -[ 93%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o -MF CMakeFiles/tree2leafnames.dir/cmdline.c.o.d -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c -[ 94%] Linking CXX executable treesize +[ 94%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o -MF CMakeFiles/reconcile.dir/cmdline.c.o.d -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.c +[ 95%] Linking CXX executable treesize cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 -[ 95%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -MD -MT src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -MF CMakeFiles/reroot.dir/cmdline.c.o.d -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.c -[ 96%] Linking CXX executable showtree -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 -[ 96%] Linking CXX executable tree2leafnames -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/treesize.dir/link.d CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 96%] Built target treesize -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/showtree.dir/link.d CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 96%] Built target showtree -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc:1: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 95%] Linking CXX executable tree2leafnames +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 +[ 95%] Built target treesize +[ 96%] Linking CXX executable showtree +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/tree2leafnames.dir/link.d CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 96%] Built target tree2leafnames @@ -4072,8 +4084,18 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 188 | catch (AnError e) { | ^ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/showtree.dir/link.d CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 96%] Built target showtree +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:9: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] + 76 | virtual void init(EdgeWeightModel& erm); + | ^~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' + 140 | virtual void init(EdgeRateModel& erm); + | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:14: + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -4094,20 +4116,6 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 37 | char *ofilename = "mpr.out"; - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 128 | catch (AnError e) { - | ^ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:9: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:76:18: warning: 'virtual void beep::EdgeWeightHandler::init(beep::EdgeWeightModel&)' was hidden [-Woverloaded-virtual=] - 76 | virtual void init(EdgeWeightModel& erm); - | ^~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.hh:140:18: note: by 'virtual void beep::EdgeTimeRateHandler::init(beep::EdgeRateModel&)' - 140 | virtual void init(EdgeRateModel& erm); - | ^~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: @@ -4231,22 +4239,36 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:27: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] 55 | static const Real ABS_TOL = 1e-6; | ^~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:2: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] - 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by 'beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)' - 23 | class BirthDeathMCMC : public StdMCMCModel, - | ^~~~~~~~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:7: +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' + 55 | Probability operator()(const Real& x) const; + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 31 | class EdgeDiscPtMapIterator : public std::iterator + | ^~~~~~~~ +In file included from /usr/include/c++/15/bits/stl_algobase.h:65, + from /usr/include/c++/15/algorithm:62, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] + 42 | std::iterator(), + | ^~~~~~~~ +/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here + 129 | struct _GLIBCXX17_DEPRECATED iterator + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.hh:6, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:14: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); | ^ @@ -4267,6 +4289,13 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 37 | char *ofilename = "mpr.out"; + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 128 | catch (AnError e) { + | ^ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:15: @@ -4300,132 +4329,6 @@ 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:25: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 197 | catch(AnError e) - | ^ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:10: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] - 58 | virtual Tree& operator=(const Tree& T); - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:28, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:9: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:14: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' - 24 | HybridTree& operator=(const HybridTree& T); - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaDensity.hh:55:17: note: by 'virtual beep::Probability beep::GammaDensity::operator()(const beep::Real&) const' - 55 | Probability operator()(const Real& x) const; - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] - 333 | virtual std::string subtree4os(Node* v, int indent) const; - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] - 329 | virtual std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:29: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:31:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 31 | class EdgeDiscPtMapIterator : public std::iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' - 108 | std::string subtree4os(Node *v, std::string indent_left, - | ^~~~~~~~~~ -In file included from /usr/include/c++/15/bits/stl_algobase.h:65, - from /usr/include/c++/15/algorithm:62, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:1: -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] - 269 | virtual Real imbalance(); - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' - 94 | Real imbalance() const; - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] - 316 | virtual Real imbalance(Node *v); - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' - 94 | Real imbalance() const; - | ^~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] - 146 | virtual Node* addNode(Node *leftChild, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' - 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] - 151 | virtual Node* addNode(Node *leftChild, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' - 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, - | ^~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator(beep::EdgeDiscPtMap*, beep::EdgeDiscretizer::Point)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:42:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] - 42 | std::iterator(), - | ^~~~~~~~ -/usr/include/c++/15/bits/stl_iterator_base_types.h:129:34: note: declared here - 129 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] - 76 | switch(args_info.input_format_arg) - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 181 | catch (AnError e) { - | ^ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:27: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 28 | NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 29 | NodeMap(const Tree &G); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 30 | NodeMap(const Tree &G, const C defval); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] - 31 | NodeMap(const NodeMap &nm); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] - 32 | ~NodeMap(); - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] - 52 | Probability operator()(const Real& x, const Real& interval) const; - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:28: -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' - 63 | Probability operator()(const Real& x) const; - | ^~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh: In constructor 'beep::EdgeDiscPtMapIterator::EdgeDiscPtMapIterator()': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscPtMapIterator.hh:54:22: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 54 | std::iterator(), @@ -4472,6 +4375,10 @@ 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. @@ -4479,6 +4386,30 @@ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:27: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:27: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 28 | NodeMap(); @@ -4500,6 +4431,14 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:2: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.hh:49:30: warning: 'virtual beep::BirthDeathProbs& beep::BirthDeathProbs::operator=(const beep::BirthDeathProbs&)' was hidden [-Woverloaded-virtual=] + 49 | virtual BirthDeathProbs& operator=(const BirthDeathProbs& dsp); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.hh:23:9: note: by 'beep::BirthDeathMCMC& beep::BirthDeathMCMC::operator=(const beep::BirthDeathMCMC&)' + 23 | class BirthDeathMCMC : public StdMCMCModel, + | ^~~~~~~~~~~~~~ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] 52 | Probability operator()(const Real& x, const Real& interval) const; | ^~~~~~~~ @@ -4507,48 +4446,146 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' 63 | Probability operator()(const Real& x) const; | ^~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:172:91: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 172 | pair edgeRateMeanVar = Options.getDoubleX2("EdgeRateParams"); - | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.hh:52:17: warning: 'virtual beep::Probability beep::Density2P_common::operator()(const beep::Real&, const beep::Real&) const' was hidden [-Woverloaded-virtual=] + 52 | Probability operator()(const Real& x, const Real& interval) const; + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:28: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.hh:63:17: note: by 'virtual beep::Probability beep::UniformDensity::operator()(const beep::Real&) const' + 63 | Probability operator()(const Real& x) const; + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationModel.hh:10, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.hh:4, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.hh:7, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:7: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 28 | NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:28:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 29 | NodeMap(const Tree &G); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:29:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 30 | NodeMap(const Tree &G, const C defval); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:30:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] + 31 | NodeMap(const NodeMap &nm); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:31:15: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: warning: template-id not allowed for destructor in C++20 [-Wtemplate-id-cdtor] + 32 | ~NodeMap(); + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ [ 97%] Linking CXX executable chainsaw cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 -[ 97%] Linking CXX executable reconcile -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chainsaw.dir/link.d CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 97%] Built target chainsaw -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/reconcile.dir/link.d CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 97%] Built target reconcile /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc: In function 'int main(int, char**)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:101:65: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 101 | pair bdr = Options.getDoubleX2("BDRates"); | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:25: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 197 | catch(AnError e) + | ^ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/chainsaw.dir/link.d CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:172:91: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 172 | pair edgeRateMeanVar = Options.getDoubleX2("EdgeRateParams"); + | ^ +[ 97%] Built target chainsaw +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:13, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/BranchSwapping.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:10: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:58:19: warning: 'virtual beep::Tree& beep::Tree::operator=(const beep::Tree&)' was hidden [-Woverloaded-virtual=] + 58 | virtual Tree& operator=(const Tree& T); + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:14: +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:24:17: note: by 'beep::HybridTree& beep::HybridTree::operator=(const beep::HybridTree&)' + 24 | HybridTree& operator=(const HybridTree& T); + | ^~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:329:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 329 | virtual std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:333:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int) const' was hidden [-Woverloaded-virtual=] + 333 | virtual std::string subtree4os(Node* v, int indent) const; + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:327:25: warning: 'virtual std::string beep::Tree::subtree4os(beep::Node*, int, bool, bool, bool, bool) const' was hidden [-Woverloaded-virtual=] + 327 | virtual std::string subtree4os(Node *v, int indent, bool useET, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:108:17: note: by 'std::string beep::HybridTree::subtree4os(beep::Node*, std::string, std::string, bool, bool, bool) const' + 108 | std::string subtree4os(Node *v, std::string indent_left, + | ^~~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:316:18: warning: 'virtual beep::Real beep::Tree::imbalance(beep::Node*)' was hidden [-Woverloaded-virtual=] + 316 | virtual Real imbalance(Node *v); + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' + 94 | Real imbalance() const; + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:269:18: warning: 'virtual beep::Real beep::Tree::imbalance()' was hidden [-Woverloaded-virtual=] + 269 | virtual Real imbalance(); + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:94:10: note: by 'beep::Real beep::HybridTree::imbalance() const' + 94 | Real imbalance() const; + | ^~~~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:151:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, std::string)' was hidden [-Woverloaded-virtual=] + 151 | virtual Node* addNode(Node *leftChild, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' + 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.hh:146:19: warning: 'virtual beep::Node* beep::Tree::addNode(beep::Node*, beep::Node*, unsigned int, std::string)' was hidden [-Woverloaded-virtual=] + 146 | virtual Node* addNode(Node *leftChild, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.hh:36:11: note: by 'beep::Node* beep::HybridTree::addNode(beep::Node*, beep::Node*, unsigned int, std::string, bool)' + 36 | Node* addNode(Node* leftChild, Node* rightChild, unsigned ID, + | ^~~~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] + 76 | switch(args_info.input_format_arg) + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 181 | catch (AnError e) { + | ^ [ 97%] Linking CXX executable primeGEM cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 +[ 97%] Linking CXX executable reconcile +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeGEM.dir/link.d CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 97%] Built target primeGEM +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/reconcile.dir/link.d CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 97%] Built target reconcile [ 98%] Linking CXX executable reroot cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/reroot.dir/link.d CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 98%] Built target reroot -[ 99%] Linking CXX executable primeDTLSR -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 -[100%] Linking CXX executable primeDLRS +[ 99%] Linking CXX executable primeDLRS cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeDLRS.dir/link.d CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 +make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 99%] Built target primeDLRS +[100%] Linking CXX executable primeDTLSR +cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDTLSR.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeDTLSR.dir/link.d CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -o primeDTLSR -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [100%] Built target primeDTLSR -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -Wl,--dependency-file=CMakeFiles/primeDLRS.dir/link.d CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so /usr/lib/aarch64-linux-gnu/liblapack.so /usr/lib/aarch64-linux-gnu/libblas.so /usr/lib/aarch64-linux-gnu/libxml2.so /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.83.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.83.0 -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[100%] Built target primeDLRS make[2]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' - dh_auto_test -O--buildsystem=cmake +dh: command-omitted: The call to "dh_auto_test -O--buildsystem=cmake" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake @@ -4637,12 +4674,14 @@ 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/2010628/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2010628/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/3662945 and its subdirectories -I: Current time: Wed Nov 19 20:23:10 -12 2025 -I: pbuilder-time-stamp: 1763626990 +I: removing directory /srv/workspace/pbuilder/2010628 and its subdirectories +I: Current time: Thu Dec 24 04:48:23 +14 2026 +I: pbuilder-time-stamp: 1798037303