Diff of the two buildlogs: -- --- b1/build.log 2025-02-11 13:18:25.191374794 +0000 +++ b2/build.log 2025-02-11 13:20:27.085918696 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Feb 11 01:16:19 -12 2025 -I: pbuilder-time-stamp: 1739279779 +I: Current time: Tue Mar 17 09:41:28 +14 2026 +I: pbuilder-time-stamp: 1773690088 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,52 +31,84 @@ dpkg-source: info: applying openmpi5.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1725934/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1719355/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 Mar 16 19:41 /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/1719355/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1719355/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='42c515622fbd4d6d8c9aa0655075b1a4' - 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='1725934' - PS1='# ' - PS2='> ' + INVOCATION_ID=6ab335267a5c472e871b4a84eb752408 + 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=1719355 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.BCyl2xwX/pbuilderrc_hOKM --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BCyl2xwX/b1 --logfile b1/build.log prime-phylo_1.0.11-13.dsc' - SUDO_GID='109' - 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.BCyl2xwX/pbuilderrc_ykHE --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BCyl2xwX/b2 --logfile b2/build.log prime-phylo_1.0.11-13.dsc' + SUDO_GID=109 + 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 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1725934/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1719355/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -319,7 +351,7 @@ Get: 179 http://deb.debian.org/debian trixie/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB] Get: 180 http://deb.debian.org/debian trixie/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB] Get: 181 http://deb.debian.org/debian trixie/main arm64 libxml2-dev arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [751 kB] -Fetched 163 MB in 1s (206 MB/s) +Fetched 163 MB in 1s (278 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 ... 19920 files and directories currently installed.) @@ -909,8 +941,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Feb 11 13:17:00 UTC 2025. -Universal Time is now: Tue Feb 11 13:17:00 UTC 2025. +Local time is now: Mon Mar 16 19:42:01 UTC 2026. +Universal Time is now: Mon Mar 16 19:42:01 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-serialization1.83.0:arm64 (1.83.0-4) ... @@ -1091,7 +1123,11 @@ Building tag database... -> Finished parsing the build-deps 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_1.0.11-13_source.changes +I: user script /srv/workspace/pbuilder/1719355/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1719355/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_1.0.11-13_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-13 dpkg-buildpackage: info: source distribution unstable @@ -1231,7 +1267,7 @@ Using the old result for compatibility since the policy is not set. This warning is for project developers. Use -Wno-dev to suppress it. --- Configuring done (6.6s) +-- Configuring done (7.2s) 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 @@ -1266,27 +1302,29 @@ 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 +[ 1%] [FLEX][MyScanner2] Building scanner with flex 2.6.4 +[ 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/flex -o/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c seqreader.l 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] 259 | darwin_entry : TEXT {$$ = NULL; /* Not implemented yet */} | ^~~~~~~~~~~~ -[ 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 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/libraries/sfile /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/libraries/sfile /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/DependInfo.cmake "--color=" 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 +[ 1%] 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/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/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 -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/sfile.c.o +[ 2%] 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/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/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 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 +gb.y: In function 'add_to_seq': +gb.y:403:9: warning: unused variable 'new_buf' [-Wunused-variable] /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] 265 | printf("%9d", char_counter + 1); @@ -1296,8 +1334,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ -gb.y: In function 'add_to_seq': -gb.y:403:9: warning: unused variable 'new_buf' [-Wunused-variable] seqreader.l: In function 'seq_read': seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c: At top level: @@ -1327,8 +1363,8 @@ [ 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' +[ 4%] [BISON][MyParser] Building parser with bison 3.8.2 [ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 -[ 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 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 NHXparse.y:108.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] @@ -1338,26 +1374,30 @@ 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' -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o -[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -[ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -cd 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-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/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 -[ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Hacks.cc.o cd 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-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/NHXparse.c.o -MF CMakeFiles/prime-phylo.dir/NHXparse.c.o.d -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c -[ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd 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-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 +[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.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 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src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o -MF CMakeFiles/prime-phylo.dir/Beep.cc.o.d -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.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/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 -[ 11%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ODESolver.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/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 +[ 11%] 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/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 +[ 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/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 +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 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c:155:32: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=] 155 | fprintf(stderr, "BW:\t%d\n", l->arg.t); @@ -1365,12 +1405,6 @@ | | | | int double | %f -[ 11%] 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/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 -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': -/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); - | ^ 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] NHXparse.y:19:36: note: expected 'char *' but argument is of type 'const char *' @@ -1380,8 +1414,10 @@ /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c:1554:17: warning: 'yyunput' defined but not used [-Wunused-function] 1554 | static void yyunput (int c, char * yy_bp ) | ^~~~~~~ -[ 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 +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c: In function 'new_annotation': +/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 @@ -1392,14 +1428,14 @@ 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/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 [ 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) - | ^ -[ 16%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscTree.cc.o -cd 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-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 -[ 16%] 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 +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; @@ -1509,16 +1545,16 @@ /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; | ^~ +/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 +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 -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) - | ^ [ 17%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscTree.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/EdgeDiscTree.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscTree.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscTree.cc [ 18%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochPtMaps.cc.o @@ -1565,17 +1601,13 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -[ 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/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; - | ^~~~~~~~~~~~~~~~ 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; | ^~~~~~~~~~~~~~~~ +[ 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/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(); @@ -1599,6 +1631,10 @@ /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 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 +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; + | ^~~~~~~~~~~~~~~~ [ 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 [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o @@ -1644,8 +1680,6 @@ 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/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, @@ -1662,7 +1696,6 @@ 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 '< >' -[ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o /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); | ^ @@ -1671,7 +1704,12 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 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 +[ 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 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const beep::Real&)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] 26 | old_times(NULL), @@ -1693,18 +1731,16 @@ /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. | ~~~~~~~~~^~~~~~~ -[ 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 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_common.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeRateMCMC_common.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.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; - | ^~~~ [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeRateModel_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/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: @@ -1736,6 +1772,10 @@ /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; | ^~~~~~~~ +[ 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 /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); @@ -1743,10 +1783,6 @@ /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); | ^~~~~~ -[ 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 @@ -1757,12 +1793,6 @@ /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++) | ~~^~~~~~~~~~ -[ 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/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: @@ -1772,6 +1802,10 @@ /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; | ^~~~~~~~ +[ 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 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$\pi\f$ @@ -1784,12 +1818,14 @@ /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; | ^~~~~~~~ +[ 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 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$. | ^~ -[ 38%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -cd /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/prime-phylo-1.0.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -MD -MT src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/DummyMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/DummyMCMC.cc In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc:1: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const beep::Real beep::NormalDensity::pi' of non-integral type [-fpermissive] 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. @@ -1837,8 +1873,6 @@ 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/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 [ 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 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$. @@ -1862,6 +1896,8 @@ /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/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 /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)': @@ -1878,10 +1914,6 @@ 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/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 [ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.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/EdgeDiscBDMCMC.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDMCMC.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDMCMC.cc -[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.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/EdgeDiscBDProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc -[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.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/EdgeDiscGSR.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.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, @@ -1907,6 +1939,12 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 49%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.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/EdgeDiscBDProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscBDProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc +[ 50%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeDiscGSR.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/EdgeDiscGSR.cc.o -MF CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o.d -o CMakeFiles/prime-phylo.dir/EdgeDiscGSR.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc +[ 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 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, @@ -1932,8 +1970,6 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 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 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc:337:27: warning: operation on 'i' may be undefined [-Wsequence-point] 337 | p[++i] = geneFams[i]->initStateProb();//updateDataProbability(); @@ -1950,38 +1986,8 @@ | ^~~~~~~~~~~~~~ [ 51%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochBDTProbs.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/EpochBDTProbs.cc.o -MF CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o.d -o CMakeFiles/prime-phylo.dir/EpochBDTProbs.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.cc -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++/14/bits/stl_algobase.h:65, - from /usr/include/c++/14/bits/specfun.h:43, - from /usr/include/c++/14/cmath:3906, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: -/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here - 127 | struct _GLIBCXX17_DEPRECATED iterator - | ^~~~~~~~ +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.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/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 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: @@ -2093,8 +2099,6 @@ /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; | ^~ -[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.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/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 In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.hh:4, @@ -2138,6 +2142,38 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +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++/14/bits/stl_algobase.h:65, + from /usr/include/c++/14/bits/specfun.h:43, + from /usr/include/c++/14/cmath:3906, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscBDProbs.cc:2: +/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | 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++/14/bits/stl_iterator_base_types.h:127:34: note: declared here + 127 | 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; @@ -2148,8 +2184,6 @@ /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, | ^~~~~~~~~~~ -[ 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 /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++) { @@ -2163,12 +2197,12 @@ /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(); | ^~~~~~ +[ 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 /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); | ^~~~~~~~ -[ 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: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; @@ -2179,10 +2213,8 @@ /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; | ^~~~~~~ -[ 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 -[ 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 +[ 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/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] @@ -2293,20 +2325,10 @@ /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.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/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; - | ^~~~~~~ -[ 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 +[ 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 +[ 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] @@ -2417,6 +2439,20 @@ /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.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/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; + | ^~~~~~~ +[ 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/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; @@ -2476,6 +2512,8 @@ 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 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_BirthDeathMCMC.hh:7, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.cc:1: @@ -2485,6 +2523,14 @@ /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 | ^~~~~~~~~~~~~~~~~~~~~~~ +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 + | ^~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -2515,18 +2561,6 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM_BirthDeathMCMC.hh:18:9: note: by 'beep::fastGEM_BirthDeathMCMC& beep::fastGEM_BirthDeathMCMC::operator=(const beep::fastGEM_BirthDeathMCMC&)' 18 | class fastGEM_BirthDeathMCMC : public StdMCMCModel, | ^~~~~~~~~~~~~~~~~~~~~~ -[ 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 -[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.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/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 -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 - | ^~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -2557,14 +2591,10 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -[ 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 -[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o /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); | ^~~~~~~~~~~ -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 /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'void beep::fastGEM::printSa()': /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1298:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable] 1298 | Real zeroTotalQuotient = 0.0; @@ -2577,14 +2607,8 @@ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable] 1356 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ -[ 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 -[ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeModel.cc.o -[ 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/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 -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 -[ 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 +[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.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/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 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, @@ -2609,16 +2633,29 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 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 +[ 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 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-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 [ 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 [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.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/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/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 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, - from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.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(); | ^ @@ -2639,15 +2676,9 @@ 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/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 -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$. - | ^~ 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: + 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(); | ^ @@ -2670,7 +2701,8 @@ /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/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/ReconciledTreeTimeMCMC.hh:5, + from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.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(); | ^ @@ -2716,7 +2748,8 @@ 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/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(); | ^ @@ -2737,15 +2770,18 @@ 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(); - | ^ +/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/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$. + | ^~ 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: + 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(); | ^ @@ -2766,16 +2802,14 @@ 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/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(); + | ^ [ 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 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: @@ -2799,10 +2833,8 @@ 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 -[ 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 +[ 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 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: @@ -2826,6 +2858,30 @@ 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/ReconciliationTimeSampler.cc: In member function 'const std::string beep::ReconciliationTimeSampler::table4os() const': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] + 422 | typedef std::map::const_iterator MapIter; + | ^~~~~~~ +[ 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/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; + | ^~~~~~~~ +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=] + 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); + | ^~~~~~~~ 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: @@ -2853,42 +2909,14 @@ /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:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc: In member function 'const std::string beep::ReconciliationTimeSampler::table4os() const': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] - 422 | 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=] - 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); - | ^~~~~~~~ -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; - | ^~~~~~~~ +[ 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 [ 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 [ 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 [ 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 -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); - | ^~~~~~~~ [ 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/EdgeDiscGSR.hh:29, @@ -2928,6 +2956,16 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ +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); + | ^~~~~~~~ +[ 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/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=] @@ -2936,25 +2974,10 @@ /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); | ^~~~~~~~ -[ 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 [ 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 -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: -/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); - | ^~~~~~~~ -[ 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 /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) @@ -2962,14 +2985,16 @@ 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/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/HybridTreeInputOutput.cc:5: +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); | ^~~~~~~~ +[ 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, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.hh:4, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:1: @@ -2996,30 +3021,24 @@ 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/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/BDHybridTreeGenerator.cc:6: +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); | ^~~~~~~~ -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); - | ^~~~~~~~ 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/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/BirthDeathInHybridProbs.cc:7: +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); | ^~~~~~~~ @@ -3036,6 +3055,14 @@ /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/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); + | ^~~~~~~~ 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=] @@ -3046,6 +3073,15 @@ 24 | HybridTree& operator=(const HybridTree& T); | ^~~~~~~~ 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/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); + | ^~~~~~~~ +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, from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc:1: @@ -3056,8 +3092,28 @@ /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); | ^~~~~~~~ +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=] + 58 | virtual Tree& operator=(const Tree& T); + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: +/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); + | ^~~~~~~~ [ 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/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); + | ^~~~~~~~ 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] @@ -3080,6 +3136,8 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' +[ 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/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: @@ -3090,28 +3148,7 @@ /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); | ^~~~~~~~ -[ 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/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=] - 58 | virtual Tree& operator=(const Tree& T); - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc:4: -/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); - | ^~~~~~~~ -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); - | ^~~~~~~~ -[ 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 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=] @@ -3120,10 +3157,13 @@ /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); | ^~~~~~~~ -[ 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: /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=] @@ -3143,18 +3183,14 @@ /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; | ^~~~~~~~ -[ 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 /usr/include/c++/14/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++/14/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 \ | ^~~~~~~ -[ 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 [ 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 [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o @@ -3169,13 +3205,10 @@ 32 | MatrixCache(const MatrixCache &C); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixCache.hh:32:23: note: remove the '< >' -[ 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/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: + 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(); | ^ @@ -3196,10 +3229,15 @@ 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/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 +[ 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 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: + 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(); | ^ @@ -3220,10 +3258,6 @@ 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: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, @@ -3235,14 +3269,7 @@ /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); | ^~~~~~~~ -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; - | ^~~~~ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:147:17: note: by 'std::string beep::FastCacheSubstitutionModel::print(bool) const' - 147 | std::string print(bool estimateRates = false) const; - | ^~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: +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. | ^~~ @@ -3257,10 +3284,6 @@ /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); | ^~~~~~~~ -[ 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 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] @@ -3271,6 +3294,19 @@ 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; + | ^~~~~ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.hh:147:17: note: by 'std::string beep::FastCacheSubstitutionModel::print(bool) const' + 147 | std::string print(bool estimateRates = false) const; + | ^~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.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. + | ^~~ +[ 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 @@ -3290,6 +3326,13 @@ 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/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); + | ^~~~~~~~ [ 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/LA_Matrix.cc: In constructor 'beep::LA_Matrix::LA_Matrix()': @@ -3300,13 +3343,6 @@ /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); - | ^~~~~~~~ In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.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. @@ -3327,100 +3363,96 @@ 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 -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' -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 -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.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' 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[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/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' 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 -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[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -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' -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' -[ 81%] 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 -[ 82%] Generating cmdline.c, cmdline.h -make[3]: Leaving directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build -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 -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 -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' [ 83%] Generating cmdline.c, cmdline.h -[ 84%] 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 +[ 83%] Generating cmdline.c, cmdline.h +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 +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 +[ 83%] Generating cmdline.c, cmdline.h make[3]: Leaving 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 -[ 85%] Generating cmdline.c, cmdline.h +[ 84%] Generating cmdline.c, cmdline.h make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build -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 +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/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 +[ 85%] Generating cmdline.c, cmdline.h make[3]: Leaving 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' -make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build [ 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 +make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build +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]: 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/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 [ 85%] Generating cmdline.c, cmdline.h +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 src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build 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/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/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=" make[3]: Entering directory '/build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o +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/tree2leafnames /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/tree2leafnames /build/reproducible-path/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.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/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=" +[ 85%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o +[ 86%] 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/c++ -DBOOST_MPI_DYN_LINK -DBOOST_MPI_NO_LIB -DBOOST_SERIALIZATION_DYN_LINK -DBOOST_SERIALIZATION_NO_LIB 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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 -MD -MT src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -MF CMakeFiles/primeGEM.dir/troyo.cc.o.d -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/reproducible-path/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc make[3]: Leaving 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/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/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 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-[ 91%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -[ 92%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.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 -cd /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 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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 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-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 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=] @@ -3429,6 +3461,10 @@ /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 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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 +[ 94%] 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/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=] @@ -3448,23 +3484,6 @@ /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) | ^ -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); - | ^~~~~~~~ -In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: -/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/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] - 51 | switch(args_info.input_format_arg) - | ^ -/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/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/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=] @@ -3480,22 +3499,64 @@ /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) { | ^ -[ 94%] Linking CXX executable showtree +[ 94%] 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 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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 +[ 94%] 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 +[ 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 +[ 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 -[ 95%] 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 -[ 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 +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); + | ^~~~~~~~ +In file included from /build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:9: +/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/tools/tree2leafnames/tree2leafnames.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc:51:11: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] + 51 | switch(args_info.input_format_arg) + | ^ +/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) { + | ^ +/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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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%] Linking CXX executable treesize [ 96%] Built target showtree -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 +[ 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 +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 '< >' /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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 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: + 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(); | ^ @@ -3516,9 +3577,6 @@ 32 | ~NodeMap(); | ^ /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/NodeMap.hh:32:5: note: remove the '< >' -/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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 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=] @@ -3551,25 +3609,17 @@ 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/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch] - 90 | switch(ai.guest_tree_format_arg) - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value 'host_tree_format__NULL' not handled in switch [-Wswitch] - 114 | switch(ai.host_tree_format_arg) - | ^ -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'int main(int, char**)': -/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:163:24: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 163 | catch (AnError e) { - | ^ -/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) { +/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) { | ^ -/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) - | ^ +/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++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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: @@ -3726,28 +3776,10 @@ 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/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(); - | ^ -/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/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. @@ -3776,6 +3808,13 @@ 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/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/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, @@ -3818,13 +3857,6 @@ /usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ -/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/applications/primeDLRS/primeDLRS.cc:13: /build/reproducible-path/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh: At global scope: /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] @@ -3850,17 +3882,6 @@ 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/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) { - | ^ -/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++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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. @@ -3896,6 +3917,37 @@ /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/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch] + 90 | switch(ai.guest_tree_format_arg) + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadHostTree(gengetopt_args_info&)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:114:9: warning: enumeration value 'host_tree_format__NULL' not handled in switch [-Wswitch] + 114 | switch(ai.host_tree_format_arg) + | ^ +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'int main(int, char**)': +/build/reproducible-path/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:163:24: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 163 | catch (AnError e) { + | ^ +/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) { + | ^ +/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/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"); + | ^ +[ 96%] 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 +[ 96%] 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 +/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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 reconcile +/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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 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: @@ -3906,6 +3958,7 @@ /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); | ^~~~~~~~ +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/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) @@ -3913,29 +3966,12 @@ /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) { | ^ -/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/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"); - | ^ +[ 96%] Built target primeGEM [ 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 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 /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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 -[ 97%] Linking CXX executable reconcile -/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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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' -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 -[ 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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 -rdynamic -Wl,-rpath -Wl,/usr/lib/aarch64-linux-gnu/openmpi/lib -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 -llapack -lblas -lxml2 /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 @@ -4043,12 +4079,14 @@ 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/1719355/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1719355/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/1725934 and its subdirectories -I: Current time: Tue Feb 11 01:18:24 -12 2025 -I: pbuilder-time-stamp: 1739279904 +I: removing directory /srv/workspace/pbuilder/1719355 and its subdirectories +I: Current time: Tue Mar 17 09:43:25 +14 2026 +I: pbuilder-time-stamp: 1773690205