Diff of the two buildlogs: -- --- b1/build.log 2023-04-29 09:09:06.536913537 +0000 +++ b2/build.log 2023-04-29 09:25:19.862176474 +0000 @@ -1,8 +1,2504 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 28 20:51:01 -12 2023 -I: pbuilder-time-stamp: 1682758261 +I: Current time: Sat Apr 29 23:09:14 +14 2023 +I: pbuilder-time-stamp: 1682759354 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] +tar: ./bin: time stamp 2024-05-31 06:48:20 is 34328345.03744916 s in the future +tar: ./build: time stamp 2024-05-31 06:48:39 is 34328364.03719874 s in the future +tar: ./dev/shm: time stamp 2024-06-01 04:31:05 is 34406510.03712772 s in the future +tar: ./dev/null: time stamp 2024-05-31 06:47:48 is 34328313.03695726 s in the future +tar: ./dev/zero: time stamp 2024-05-31 06:47:48 is 34328313.0368996 s in the future +tar: ./dev/full: time stamp 2024-05-31 06:47:48 is 34328313.03685456 s in the future +tar: ./dev/random: time stamp 2024-05-31 06:47:48 is 34328313.03681012 s in the future +tar: ./dev/urandom: time stamp 2024-05-31 06:47:48 is 34328313.03676466 s in the future +tar: ./dev/tty: time stamp 2024-05-31 06:47:48 is 34328313.03671956 s in the future +tar: ./dev/console: time stamp 2024-05-31 06:47:48 is 34328313.03667396 s in the future +tar: ./dev/pts: time stamp 2024-05-31 06:47:48 is 34328313.03662436 s in the future +tar: ./dev/ptmx: time stamp 2024-05-31 06:47:48 is 34328313.03658416 s in the future +tar: ./etc/resolv.conf: time stamp 2024-06-01 04:31:05 is 34406510.0364772 s in the future +tar: ./etc/mailname: time stamp 2024-06-01 04:31:05 is 34406510.03639954 s in the future +tar: ./etc/hostname: time stamp 2024-06-01 04:31:05 is 34406510.03634016 s in the future +tar: ./etc/hosts: time stamp 2024-06-01 04:31:05 is 34406510.03628208 s in the future +tar: ./etc/apt/sources.list: time stamp 2024-05-31 06:50:22 is 34328467.03609648 s in the future +tar: ./etc/apt/apt.conf.d/80proxy: time stamp 2024-05-31 06:50:22 is 34328467.03600044 s in the future +tar: ./etc/apt/apt.conf.d/15pbuilder: time stamp 2024-05-31 06:48:39 is 34328364.03584206 s in the future +tar: ./etc/apt/apt.conf.d: time stamp 2024-05-31 06:50:22 is 34328467.03580138 s in the future +tar: ./etc/apt/trusted.gpg.d: time stamp 2024-05-31 06:48:12 is 34328337.03008856 s in the future +tar: ./etc/apt: time stamp 2024-05-31 06:50:22 is 34328467.02999914 s in the future +tar: ./etc/cron.daily: time stamp 2024-05-31 06:48:55 is 34328380.02976902 s in the future +tar: ./etc/logrotate.d: time stamp 2024-05-31 06:48:55 is 34328380.02939144 s in the future +tar: ./etc/default: time stamp 2024-05-31 06:48:19 is 34328344.02235092 s in the future +tar: ./etc/dpkg/origins/default: time stamp 2024-05-31 06:47:49 is 34328314.0221334 s in the future +tar: ./etc/dpkg/origins: time stamp 2024-05-31 06:48:14 is 34328339.02209132 s in the future +tar: ./etc/dpkg/dpkg.cfg.d/02speedup: time stamp 2024-05-31 06:50:22 is 34328467.02196644 s in the future +tar: ./etc/dpkg/dpkg.cfg.d: time stamp 2024-05-31 06:50:22 is 34328467.02192704 s in the future +tar: ./etc/dpkg: time stamp 2024-05-31 06:48:39 is 34328364.02178892 s in the future +tar: ./etc/skel: time stamp 2024-05-31 06:48:14 is 34328339.02141862 s in the future +tar: ./etc/update-motd.d: time stamp 2024-05-31 06:48:14 is 34328339.02130566 s in the future +tar: ./etc/cron.d: time stamp 2024-05-31 06:48:14 is 34328339.01918342 s in the future +tar: ./etc/ld.so.conf.d: time stamp 2024-05-31 06:48:55 is 34328380.0177903 s in the future +tar: ./etc/selinux: time stamp 2024-05-31 06:48:12 is 34328337.01690624 s in the future +tar: ./etc/terminfo: time stamp 2024-05-31 06:48:13 is 34328338.01675726 s in the future +tar: ./etc/security/opasswd: time stamp 2024-05-31 06:48:19 is 34328344.01607286 s in the future +tar: ./etc/security: time stamp 2024-05-31 06:48:19 is 34328344.01602102 s in the future +tar: ./etc/pam.d/common-auth: time stamp 2024-05-31 06:48:19 is 34328344.01343638 s in the future +tar: ./etc/pam.d/common-account: time stamp 2024-05-31 06:48:19 is 34328344.01332418 s in the future +tar: ./etc/pam.d/common-password: time stamp 2024-05-31 06:48:19 is 34328344.01325896 s in the future +tar: ./etc/pam.d/common-session: time stamp 2024-05-31 06:48:19 is 34328344.01318574 s in the future +tar: ./etc/pam.d/common-session-noninteractive: time stamp 2024-05-31 06:48:19 is 34328344.01311518 s in the future +tar: ./etc/pam.d: time stamp 2024-05-31 06:48:19 is 34328344.01307508 s in the future +tar: ./etc/perl/Net: time stamp 2024-05-31 06:48:19 is 34328344.01295148 s in the future +tar: ./etc/init.d: time stamp 2024-05-31 06:48:14 is 34328339.01274556 s in the future +tar: ./etc/fstab: time stamp 2024-05-31 06:47:48 is 34328313.01267484 s in the future +tar: ./etc/opt: time stamp 2024-05-31 06:47:49 is 34328314.0125349 s in the future +tar: ./etc/timezone: time stamp 2024-05-31 06:48:13 is 34328338.0124748 s in the future +tar: ./etc/environment: time stamp 2024-05-31 06:48:19 is 34328344.01238004 s in the future +tar: ./etc/.pwd.lock: time stamp 2024-05-31 06:48:19 is 34328344.01233038 s in the future +tar: ./etc/shadow: time stamp 2024-05-31 06:48:19 is 34328344.01216036 s in the future +tar: ./etc/passwd-: time stamp 2024-05-31 06:47:49 is 34328314.01202176 s in the future +tar: ./etc/passwd: time stamp 2024-05-31 06:48:19 is 34328344.01195056 s in the future +tar: ./etc/gshadow: time stamp 2024-05-31 06:48:19 is 34328344.01183 s in the future +tar: ./etc/group-: time stamp 2024-05-31 06:47:49 is 34328314.01171574 s in the future +tar: ./etc/group: time stamp 2024-05-31 06:48:19 is 34328344.01165044 s in the future +tar: ./etc/subuid: time stamp 2024-05-31 06:48:19 is 34328344.01160248 s in the future +tar: ./etc/subgid: time stamp 2024-05-31 06:48:19 is 34328344.01155504 s in the future +tar: ./etc/shells: time stamp 2024-05-31 06:48:20 is 34328345.01149852 s in the future +tar: ./etc/gss: time stamp 2024-05-31 06:48:36 is 34328361.01140324 s in the future +tar: ./etc/ld.so.cache: time stamp 2024-05-31 06:48:55 is 34328380.00641528 s in the future +tar: ./lib: time stamp 2024-05-31 06:48:20 is 34328345.00624226 s in the future +tar: ./media: time stamp 2024-05-31 06:47:49 is 34328314.00618414 s in the future +tar: ./mnt: time stamp 2024-05-31 06:47:49 is 34328314.006137 s in the future +tar: ./opt: time stamp 2024-05-31 06:47:49 is 34328314.0060918 s in the future +tar: ./root: time stamp 2024-05-31 06:47:49 is 34328314.0059088 s in the future +tar: ./run/mount: time stamp 2024-05-31 06:47:49 is 34328314.00580012 s in the future +tar: ./run/lock: time stamp 2024-05-31 06:47:50 is 34328315.00574936 s in the future +tar: ./sbin: time stamp 2024-05-31 06:48:20 is 34328345.00570658 s in the future +tar: ./srv: time stamp 2024-05-31 06:47:49 is 34328314.0056591 s in the future +tar: ./tmp: time stamp 2024-06-01 04:31:19 is 34406524.00558366 s in the future +tar: ./usr/lib/aarch64-linux-gnu/e2fsprogs: time stamp 2024-05-31 06:47:59 is 34328324.00504658 s in the future +tar: ./usr/lib/aarch64-linux-gnu/gconv/gconv-modules.d: time stamp 2024-05-31 06:48:01 is 34328325.99847088 s in the future +tar: ./usr/lib/aarch64-linux-gnu/gconv: time stamp 2024-05-31 06:48:01 is 34328325.6774761 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/B: time stamp 2024-05-31 06:48:06 is 34328330.67605134 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/CORE: time stamp 2024-05-31 06:48:06 is 34328330.5828207 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Compress/Raw: time stamp 2024-05-31 06:48:06 is 34328330.58151766 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Data: time stamp 2024-05-31 06:48:06 is 34328330.58031952 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Devel: time stamp 2024-05-31 06:48:06 is 34328330.57139328 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Digest: time stamp 2024-05-31 06:48:06 is 34328330.57107322 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/CN: time stamp 2024-05-31 06:48:06 is 34328330.57088698 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/JP: time stamp 2024-05-31 06:48:06 is 34328330.57064716 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/KR: time stamp 2024-05-31 06:48:06 is 34328330.57050282 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/MIME/Header: time stamp 2024-05-31 06:48:06 is 34328330.56948298 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/MIME: time stamp 2024-05-31 06:48:06 is 34328330.56925042 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode/Unicode: time stamp 2024-05-31 06:48:06 is 34328330.56909264 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/5.36.0/Encode: time stamp 2024-05-31 06:48:06 is 34328330.56731526 s in the 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06:48:55 is 34328367.54464666 s in the future +tar: ./usr/lib/locale/aa_ET: time stamp 2024-05-31 06:48:55 is 34328367.5446195 s in the future +tar: ./usr/lib/locale/aa_ER@saaho/LC_MESSAGES: time stamp 2024-05-31 06:48:55 is 34328367.5445896 s in the future +tar: ./usr/lib/locale/aa_ER@saaho: time stamp 2024-05-31 06:48:55 is 34328367.54456044 s in the future +tar: ./usr/lib/locale/aa_ER/LC_MESSAGES: time stamp 2024-05-31 06:48:55 is 34328367.5445295 s in the future +tar: ./usr/lib/locale/aa_ER: time stamp 2024-05-31 06:48:55 is 34328367.5445015 s in the future +tar: ./usr/lib/locale: time stamp 2024-05-31 06:48:54 is 34328366.54447426 s in the future +tar: ./usr/lib/apt/planners: time stamp 2024-05-31 06:47:55 is 34328307.5444452 s in the future +tar: ./usr/lib/apt: time stamp 2024-05-31 06:47:55 is 34328307.54441882 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl/cross-config-5.36.0: time stamp 2024-05-31 06:48:06 is 34328318.54438836 s in the future +tar: ./usr/lib/aarch64-linux-gnu/perl: time stamp 2024-05-31 06:47:45 is 34328297.54435848 s in the future +tar: ./usr/lib/aarch64-linux-gnu: time stamp 2024-05-31 06:48:50 is 34328362.54433076 s in the future +tar: ./usr/lib: time stamp 2024-05-31 06:48:39 is 34328351.54430346 s in the future +tar: ./usr: time stamp 2024-05-31 06:47:50 is 34328302.5442794 s in the future +tar: ./run: time stamp 2024-06-01 04:31:05 is 34406497.5442544 s in the future +tar: ./etc/systemd/system/multi-user.target.wants: time stamp 2024-05-31 06:48:15 is 34328327.5442223 s in the future +tar: ./etc/systemd/system/timers.target.wants: time stamp 2024-05-31 06:48:18 is 34328330.54419188 s in the future +tar: ./etc/systemd/system: time stamp 2024-05-31 06:48:15 is 34328327.5441645 s in the future +tar: ./etc/rcS.d: time stamp 2024-05-31 06:48:14 is 34328326.54412524 s in the future +tar: ./etc/rc6.d: time stamp 2024-05-31 06:48:14 is 34328326.54409842 s in the future +tar: ./etc/rc0.d: time stamp 2024-05-31 06:48:14 is 34328326.54407168 s in the future +tar: ./etc/alternatives: time stamp 2024-05-31 06:48:55 is 34328367.54404462 s in the future +tar: ./etc: time stamp 2024-06-01 04:31:05 is 34406497.5440195 s in the future +tar: ./dev: time stamp 2024-06-01 04:31:05 is 34406497.54385402 s in the future I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem @@ -16,7 +2512,7 @@ I: copying [./garli_2.1.orig.tar.gz] I: copying [./garli_2.1-7.debian.tar.xz] I: Extracting source -gpgv: Signature made Sun Feb 20 02:34:04 2022 -12 +gpgv: Signature made Mon Feb 21 04:34:04 2022 +14 gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./garli_2.1-7.dsc: no acceptable signature found @@ -25,52 +2521,84 @@ dpkg-source: info: unpacking garli_2.1-7.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11142/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/15721/tmp/hooks/D01_modify_environment starting +debug: Running on codethink11-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 Apr 29 23:09 /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/15721/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/15721/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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]="15" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + 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=8' - DISTRIBUTION='bookworm' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - 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='11142' - PS1='# ' - PS2='> ' + 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=15721 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.YmXTb7sD/pbuilderrc_ItWs --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YmXTb7sD/b1 --logfile b1/build.log garli_2.1-7.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + 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.YmXTb7sD/pbuilderrc_3KeQ --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.YmXTb7sD/b2 --logfile b2/build.log --extrapackages usrmerge garli_2.1-7.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink14-arm64 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 27 22:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/11142/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 31 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/15721/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -200,7 +2728,7 @@ Get: 84 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libopenmpi-dev arm64 4.1.4-3+b1 [970 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 ncl-tools arm64 2.1.21+git20210811.b1213a7-4 [184 kB] -Fetched 43.3 MB in 2s (20.8 MB/s) +Fetched 43.3 MB in 5s (9520 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package readline-common. (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 ... 19616 files and directories currently installed.) @@ -561,8 +3089,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes +I: user script /srv/workspace/pbuilder/15721/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/15721/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/garli-2.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../garli_2.1-7_source.changes dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-7 dpkg-buildpackage: info: source distribution unstable @@ -664,8 +3201,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -754,28 +3291,6 @@ garlimain.cpp:434:76: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ -In file included from /usr/include/stdio.h:906, - from /usr/include/c++/12/cstdio:42, - from /usr/include/c++/12/ext/string_conversions.h:43, - from /usr/include/c++/12/bits/basic_string.h:3960, - from /usr/include/c++/12/string:53, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from configoptions.cpp:20: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] - 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 31 | __glibc_objsize (__s), __fmt, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 32 | __va_arg_pack ()); - | ~~~~~~~~~~~~~~~~~ -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from bipartition.cpp:20: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -820,6 +3335,28 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -836,11 +3373,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -850,7 +3388,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -888,12 +3426,10 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -903,7 +3439,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -945,6 +3481,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1000,16 +3538,11 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1019,7 +3552,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1057,11 +3590,15 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i' when C++17 is enabled changed to match C++14 in GCC 10.1 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ | ^ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': -model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3675:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3675 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3677:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3677 | fread(&o, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3684:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3684 | fread((char*) &(b[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3691:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3691 | fread((char*) &(rateMults[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3692:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3692 | fread((char*) &(rateProbs[i]), sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3699:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3699 | fread((char*) &a, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3705:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3705 | fread((char*) &p, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3710:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3710 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp:3713:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 3713 | fread((char*) &x, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -model.cpp: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': -model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1563,6 +4064,42 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -2160,6 +4675,28 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/c++/12/ext/string_conversions.h:43, + from /usr/include/c++/12/bits/basic_string.h:3960, + from /usr/include/c++/12/string:53, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from configoptions.cpp:20: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:40: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] 337 | sprintf(modName, "model%d", modelNum); @@ -2181,7 +4718,7 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from funcs.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2191,7 +4728,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2229,11 +4766,16 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2243,7 +4785,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2274,11 +4816,18 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from configreader.cpp:30: + from adaptation.cpp:25: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2288,7 +4837,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2304,13 +4853,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': -reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; - | ~~~~~~~^~~~~~~~~~~~~~~~~~ -/usr/include/c++/12/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ reconnode.h: In member function 'listIt ReconList::GetFirstNodeAtDist(int)': reconnode.h:98:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 98 | return find_if(l.begin(),l.end(),bind2nd(DistEquals(), Dist)); @@ -2333,10 +4875,6 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from model.cpp:17: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2724,14 +5255,29 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from optimization.cpp:21: +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': +optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ + | ^ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp In file included from tree.h:35, - from optimization.cpp:19: + from individual.h:21, + from model.cpp:26: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from tree.h:24: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from model.cpp:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2769,17 +5315,10 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from optimization.cpp:21: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i Tree::CalcDerivativesRateHet(TreeNode*, TreeNode*)': -optimization.cpp:1099:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 1099 | pair Tree::CalcDerivativesRateHet(TreeNode *nd1, TreeNode *nd2){ - | ^ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': model.cpp:3666:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 3666 | fread(r+i, sizeof(FLOAT_TYPE), 1, in); @@ -2815,8 +5354,6 @@ model.cpp:4956:30: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 4956 | fread(dummy, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from tree.h:35, from individual.h:21, @@ -2952,10 +5489,6 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': -tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ - | ^ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -2979,6 +5512,10 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/aarch64-linux-gnu/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +tree.cpp: In member function 'std::pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE)': +tree.cpp:8463:87: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 8463 | pair Tree::OptimizeSingleSiteTreeScale(FLOAT_TYPE optPrecision){ + | ^ In file included from /usr/include/stdio.h:906, from /usr/include/c++/12/cstdio:42, from /usr/include/c++/12/ext/string_conversions.h:43, @@ -5859,7 +8396,7 @@ pass 10: -6247.0222 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6247.0222 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6156,7 +8693,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 0 minutes and 29 seconds +Time used = 0 hours, 0 minutes and 28 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6308,7 +8845,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 0 minutes and 19 seconds +Time used = 0 hours, 0 minutes and 20 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6720,7 +9257,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6882,7 +9419,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7457,7 +9994,7 @@ pass 36: -13306.2062 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) Looking for minimum length branches... Final score = -13306.2062 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 9 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9987,7 +12524,7 @@ pass 486: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 7 seconds +Time used = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13084,9 +15621,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 670, seed 1640893952, best lnL -90.230 +Bootstrap rep 1 (of 1) generation 629, seed 619464215, best lnL -90.249 gen current_lnL precision last_tree_imp -670 -90.2297 0.500 215 +629 -90.2493 0.500 215 700 -90.2169 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced @@ -13263,6 +15800,7 @@ 100 -112.9555 0.500 84 200 -112.4964 0.500 84 300 -112.3224 0.500 84 +400 -112.1061 0.500 84 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13349,10 +15887,9 @@ STARTING RUN Restarting from checkpoint... - generation 399, seed 1392391903, best lnL -112.106 + generation 450, seed 993485125, best lnL -111.951 gen current_lnL precision last_tree_imp -399 -112.1061 0.500 84 -400 -112.1061 0.500 84 +450 -111.9507 0.500 84 500 -111.8129 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced @@ -13542,6 +16079,8 @@ 1200 -111.6824 0.010 563 1300 -111.6822 0.010 563 1400 -111.6821 0.010 563 +1500 -111.6819 0.010 563 +1600 -111.6818 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13627,9 +16166,9 @@ STARTING RUN Restarting from checkpoint... - generation 1486, seed 456931584, best lnL -111.682 + generation 1632, seed 435433711, best lnL -111.682 gen current_lnL precision last_tree_imp -1486 -111.6819 0.010 563 +1632 -111.6818 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13645,7 +16184,7 @@ no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... @@ -13653,14 +16192,14 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6819 +Replicate 1 : -111.6818 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.608 +rep 1: 2.606 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log @@ -13876,9 +16415,9 @@ STARTING RUN Restarting from checkpoint... - generation 33, seed 67981921, best lnL -205.650 + generation 36, seed 214459759, best lnL -205.650 gen current_lnL precision last_tree_imp -33 -205.6499 0.500 18 +36 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 60 -205.5990 0.500 53 @@ -14160,9 +16699,9 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 32, seed 586802293, best lnL -195.278 +Bootstrap rep 1 (of 1) generation 33, seed 67981921, best lnL -195.278 gen current_lnL precision last_tree_imp -32 -195.2775 0.500 0 +33 -195.2775 0.500 0 40 -195.2554 0.500 0 50 -195.2137 0.500 0 60 -195.1628 0.500 0 @@ -14386,6 +16925,7 @@ 1200 -3352.6736 0.010 0 1300 -3352.5526 0.010 0 1400 -3352.3134 0.010 0 +1500 -3352.2739 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14489,10 +17029,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1483, seed 606078497, best lnL -3352.274 +Search rep 1 (of 2) generation 1550, seed 1891092166, best lnL -3352.269 gen current_lnL precision last_tree_imp -1483 -3352.2745 0.010 0 -1500 -3352.2739 0.010 0 +1550 -3352.2687 0.010 0 1600 -3352.1712 0.010 0 1700 -3352.1587 0.010 0 1800 -3352.0790 0.010 0 @@ -14505,62 +17044,63 @@ 2500 -3351.1213 0.010 0 2600 -3351.0591 0.010 0 2700 -3351.0589 0.010 0 +2800 -3351.0534 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... Current score = -3351.0534 Performing final optimizations... -pass 1 : -3350.9548 (branch= 0.0000 alpha= 0.0000 pinv= 0.0278 eq freqs= 0.0169 rel rates= 0.0499 subset rates= 0.0039) -pass 2 : -3350.8641 (branch= 0.0000 alpha= 0.0129 pinv= 0.0170 eq freqs= 0.0000 rel rates= 0.0607 subset rates= 0.0000) -pass 3 : -3350.7850 (branch= 0.0085 alpha= 0.0168 pinv= 0.0155 eq freqs= 0.0000 rel rates= 0.0383 subset rates= 0.0000) -pass 4 : -3350.7176 (branch= 0.0035 alpha= 0.0148 pinv= 0.0141 eq freqs= 0.0010 rel rates= 0.0314 subset rates= 0.0026) -pass 5 : -3350.6590 (branch= 0.0055 alpha= 0.0125 pinv= 0.0134 eq freqs= 0.0000 rel rates= 0.0259 subset rates= 0.0013) -pass 6 : -3350.6080 (branch= 0.0039 alpha= 0.0113 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0233 subset rates= 0.0000) -pass 7 : -3350.5614 (branch= 0.0008 alpha= 0.0113 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0215 subset rates= 0.0016) -pass 8 : -3350.5219 (branch= 0.0019 alpha= 0.0103 pinv= 0.0101 eq freqs= 0.0000 rel rates= 0.0172 subset rates= 0.0000) -pass 9 : -3350.4860 (branch= 0.0003 alpha= 0.0093 pinv= 0.0092 eq freqs= 0.0001 rel rates= 0.0160 subset rates= 0.0011) -pass 10: -3350.4547 (branch= 0.0012 alpha= 0.0086 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0132 subset rates= 0.0000) -pass 11: -3350.4274 (branch= 0.0002 alpha= 0.0077 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0119 subset rates= 0.0000) -pass 12: -3350.4029 (branch= 0.0000 alpha= 0.0073 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0105 subset rates= 0.0000) -pass 13: -3350.3811 (branch= 0.0000 alpha= 0.0066 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0091 subset rates= 0.0000) -pass 14: -3350.3620 (branch= 0.0000 alpha= 0.0060 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0078 subset rates= 0.0000) -pass 15: -3350.3452 (branch= 0.0000 alpha= 0.0053 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) -pass 16: -3350.3304 (branch= 0.0000 alpha= 0.0047 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0058 subset rates= 0.0000) -pass 17: -3350.3176 (branch= 0.0000 alpha= 0.0042 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) +pass 1 : -3350.9548 (branch= 0.0000 alpha= 0.0000 pinv= 0.0279 eq freqs= 0.0169 rel rates= 0.0500 subset rates= 0.0038) +pass 2 : -3350.8637 (branch= 0.0000 alpha= 0.0130 pinv= 0.0170 eq freqs= 0.0000 rel rates= 0.0611 subset rates= 0.0000) +pass 3 : -3350.7852 (branch= 0.0057 alpha= 0.0180 pinv= 0.0152 eq freqs= 0.0000 rel rates= 0.0396 subset rates= 0.0000) +pass 4 : -3350.7191 (branch= 0.0035 alpha= 0.0136 pinv= 0.0143 eq freqs= 0.0010 rel rates= 0.0308 subset rates= 0.0029) +pass 5 : -3350.6593 (branch= 0.0064 alpha= 0.0129 pinv= 0.0133 eq freqs= 0.0000 rel rates= 0.0253 subset rates= 0.0020) +pass 6 : -3350.6076 (branch= 0.0034 alpha= 0.0111 pinv= 0.0123 eq freqs= 0.0003 rel rates= 0.0235 subset rates= 0.0011) +pass 7 : -3350.5628 (branch= 0.0032 alpha= 0.0106 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0196 subset rates= 0.0000) +pass 8 : -3350.5222 (branch= 0.0005 alpha= 0.0102 pinv= 0.0101 eq freqs= 0.0000 rel rates= 0.0185 subset rates= 0.0013) +pass 9 : -3350.4866 (branch= 0.0013 alpha= 0.0095 pinv= 0.0092 eq freqs= 0.0001 rel rates= 0.0155 subset rates= 0.0000) +pass 10: -3350.4558 (branch= 0.0002 alpha= 0.0085 pinv= 0.0083 eq freqs= 0.0000 rel rates= 0.0138 subset rates= 0.0000) +pass 11: -3350.4269 (branch= 0.0000 alpha= 0.0082 pinv= 0.0074 eq freqs= 0.0000 rel rates= 0.0123 subset rates= 0.0009) +pass 12: -3350.4025 (branch= 0.0008 alpha= 0.0071 pinv= 0.0067 eq freqs= 0.0001 rel rates= 0.0098 subset rates= 0.0000) +pass 13: -3350.3813 (branch= 0.0001 alpha= 0.0062 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0088 subset rates= 0.0000) +pass 14: -3350.3623 (branch= 0.0000 alpha= 0.0058 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0078 subset rates= 0.0000) +pass 15: -3350.3454 (branch= 0.0000 alpha= 0.0053 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0068 subset rates= 0.0000) +pass 16: -3350.3306 (branch= 0.0000 alpha= 0.0047 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0059 subset rates= 0.0000) +pass 17: -3350.3176 (branch= 0.0000 alpha= 0.0042 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0051 subset rates= 0.0000) pass 18: -3350.3063 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0043 subset rates= 0.0000) pass 19: -3350.2965 (branch= 0.0000 alpha= 0.0032 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0037 subset rates= 0.0000) -pass 20: -3350.2879 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) +pass 20: -3350.2879 (branch= 0.0000 alpha= 0.0028 pinv= 0.0025 eq freqs= 0.0000 rel rates= 0.0032 subset rates= 0.0000) optimization up to ... -pass 30: -3350.2455 (branch= 0.0000 alpha= 0.0142 pinv= 0.0129 eq freqs= 0.0000 rel rates= 0.0154 subset rates= 0.0000) +pass 30: -3350.2452 (branch= 0.0000 alpha= 0.0141 pinv= 0.0128 eq freqs= 0.0000 rel rates= 0.0157 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2359 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 40: -3350.2356 (branch= 0.0000 alpha= 0.0030 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0037 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2339 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 60: -3350.2332 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 61: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 65: -3350.2331 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2335 +Final score = -3350.2331 Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.106, AG = 10.382, AT = 2.681, CG = 0.001, CT = 21.820, GT = 1.000 + AC = 3.113, AG = 10.408, AT = 2.687, CG = 0.001, CT = 21.903, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3329 0.2222 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5780 + 0.5770 with an invariant (invariable) site category, proportion estimated - 0.3657 + 0.3655 Substitution rate categories under this model: rate proportion - 0.0000 0.3657 - 0.0486 0.1586 - 0.2998 0.1586 - 0.8697 0.1586 - 2.7819 0.1586 + 0.0000 0.3655 + 0.0484 0.1586 + 0.2992 0.1586 + 0.8691 0.1586 + 2.7832 0.1586 Model 2 Number of states = 2 (binary data) @@ -14585,20 +17125,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2335 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.106 10.38 2.681 0.001 21.82 1 0.333 0.222 0.157 0.288 0.578 0.366 +rep 1: 3.113 10.41 2.687 0.001 21.9 1 0.333 0.222 0.157 0.288 0.577 0.365 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.788 1.820 0.180 +rep 1: 0.789 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14848,9 +17388,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 426, seed 607929584, best lnL -3323.902 +Search rep 1 (of 2) generation 421, seed 781746381, best lnL -3323.906 gen current_lnL precision last_tree_imp -426 -3323.9019 0.500 1 +421 -3323.9056 0.500 1 500 -3323.6818 0.500 1 600 -3323.3459 0.500 1 Optimization precision reduced @@ -15102,6 +17642,7 @@ 5800 -210.4709 0.010 1104 6000 -210.4362 0.010 1104 6200 -210.4333 0.010 1104 +6400 -210.3827 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15181,11 +17722,9 @@ STARTING RUN Restarting from checkpoint... - generation 6212, seed 1898667431, best lnL -210.427 + generation 6472, seed 368622547, best lnL -210.383 gen current_lnL precision last_tree_imp -6212 -210.4269 0.010 1104 -6300 -210.3893 0.010 1104 -6400 -210.3827 0.010 1104 +6472 -210.3827 0.010 1104 6500 -210.3682 0.010 1104 6600 -210.3672 0.010 1104 6700 -210.3649 0.010 1104 @@ -15407,9 +17946,6 @@ 5600 -165.6911 0.010 843 5800 -165.5806 0.010 843 6000 -165.5430 0.010 843 -6200 -165.4993 0.010 843 -6400 -165.3818 0.010 843 -6600 -165.3041 0.010 843 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15490,9 +18026,14 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 6693, seed 1381377876, best lnL -165.290 +Bootstrap rep 1 (of 1) generation 6158, seed 1915565135, best lnL -165.499 gen current_lnL precision last_tree_imp -6693 -165.2904 0.010 843 +6158 -165.4993 0.010 843 +6200 -165.4993 0.010 843 +6300 -165.4042 0.010 843 +6400 -165.3818 0.010 843 +6500 -165.3290 0.010 843 +6600 -165.3041 0.010 843 6700 -165.2904 0.010 843 6800 -165.1797 0.010 6750 6900 -165.1509 0.010 6750 @@ -15721,15 +18262,55 @@ 8600 -212.6460 0.010 3769 8800 -212.5920 0.010 3769 9000 -212.5542 0.010 3769 -NOTE: ****Specified time limit (5 seconds) reached... +9200 -212.5387 0.010 3769 +9400 -212.5218 0.010 3769 +9600 -212.5169 0.010 3769 +9800 -212.5127 0.010 3769 +10000 -212.5054 0.010 3769 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +NOTE: ****Specified generation limit (10000) reached... -NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY -TERMINATED. OUTPUT FILES (tree files, etc.) WILL NOT BE -FINALIZED SO THAT THE RUN CAN BE RESTARTED WHERE IT LEFT OFF -(set restart = 1 in the config file). IF YOU WANT TO USE THE -PARTIAL OUTPUT FILES WITHOUT RESTARTING YOU WILL NEED TO MANUALLY -ADD "end;" TO THE TREE FILES. +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +Model 1 + Number of states = 4 (nucleotide data) + Nucleotide Relative Rate Matrix: 6 rates + AC = 7.773, AG = 14.654, AT = 0.614, CG = 14.717, CT = 9.694, GT = 1.000 + Equilibrium State Frequencies: estimated + (ACGT) 0.2198 0.2879 0.1846 0.3077 + Rate Heterogeneity Model: + no rate heterogeneity + +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 1 branches were collapsed. + +Saving site likelihoods to file ch.n.sitelikes.log ... +WARNING: Site likelihoods being output on prematurely terminated search ... + +NOTE: ***Search was terminated before full auto-termination condition was reached! +Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** + + +####################################################### + +Completed 1 replicate search(es) (of 1). +Results: +Replicate 1 : -212.5054 + +Parameter estimates: + r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) +rep 1: 7.773 14.65 0.6135 14.72 9.694 1 0.220 0.288 0.185 0.308 +Treelengths: + TL +rep 1: 1.727 + +Saving final tree from best search rep (#1) to ch.n.best.tre +Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log + +WARNING: Internal states inferred on tree from prematurely terminated search + +####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15800,24 +18381,17 @@ STARTING RUN Restarting from checkpoint... - generation 9062, seed 1902281475, best lnL -212.549 + generation 10001, seed 1459438551, best lnL -212.505 gen current_lnL precision last_tree_imp -9062 -212.5491 0.010 3769 -9100 -212.5473 0.010 3769 -9200 -212.5387 0.010 3769 -9300 -212.5373 0.010 3769 -9400 -212.5218 0.010 3769 -Reached termination condition! -last topological improvement at gen 3769 -Improvement over last 500 gen = 0.04921 +10001 -212.5054 0.010 3769 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 7.445, AG = 14.261, AT = 0.625, CG = 14.296, CT = 9.213, GT = 1.000 + AC = 7.773, AG = 14.654, AT = 0.614, CG = 14.717, CT = 9.694, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2201 0.2884 0.1832 0.3082 + (ACGT) 0.2198 0.2879 0.1846 0.3077 Rate Heterogeneity Model: no rate heterogeneity @@ -15830,15 +18404,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.5218 +Replicate 1 : -212.5054 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 7.445 14.26 0.6255 14.3 9.213 1 0.220 0.288 0.183 0.308 +rep 1: 7.773 14.65 0.6135 14.72 9.694 1 0.220 0.288 0.185 0.308 Treelengths: TL -rep 1: 1.728 +rep 1: 1.727 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -15997,9 +18571,6 @@ 6800 -210.2615 0.010 2883 7000 -210.2578 0.010 2883 7200 -210.2570 0.010 2883 -7400 -210.2287 0.010 2883 -7600 -210.2174 0.010 2883 -7800 -210.1381 0.010 7783 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16087,52 +18658,33 @@ STARTING RUN Restarting from checkpoint... - generation 7886, seed 990274145, best lnL -210.132 + generation 7224, seed 1590541792, best lnL -210.257 gen current_lnL precision last_tree_imp -7886 -210.1315 0.010 7783 -7900 -210.1315 0.010 7783 -8000 -210.1299 0.010 7783 -8100 -210.1283 0.010 7783 -8200 -210.1281 0.010 7783 -8300 -210.1179 0.010 7783 -8400 -210.1159 0.010 7783 -8500 -210.0805 0.010 7783 -8600 -210.0640 0.010 7783 -8700 -210.0387 0.010 7783 -8800 -209.9972 0.010 7783 -8900 -209.9879 0.010 7783 -9000 -209.9555 0.010 7783 -9100 -209.9409 0.010 7783 -9200 -209.9334 0.010 7783 -9300 -209.9308 0.010 7783 -9400 -209.9299 0.010 7783 -9500 -209.9156 0.010 7783 -9600 -209.9156 0.010 7783 -9700 -209.9019 0.010 7783 -9800 -209.8954 0.010 7783 +7224 -210.2570 0.010 2883 +7300 -210.2289 0.010 2883 Reached termination condition! -last topological improvement at gen 7783 -Improvement over last 500 gen = 0.03545 +last topological improvement at gen 2883 +Improvement over last 500 gen = 0.03262 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.485, AG = 4.605, AT = 0.214, CG = 4.763, CT = 8.462, GT = 1.000 + AC = 2.168, AG = 4.088, AT = 0.193, CG = 3.926, CT = 7.381, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2432 0.3351 0.2122 0.2095 + (ACGT) 0.2401 0.3369 0.2133 0.2096 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.2903 + 1.5973 with an invariant (invariable) site category, proportion estimated - 0.2309 + 0.2011 Substitution rate categories under this model: rate proportion - 0.0000 0.2309 - 0.3256 0.1923 - 0.6827 0.1923 - 1.0758 0.1923 - 1.9158 0.1923 + 0.0000 0.2011 + 0.2400 0.1997 + 0.6040 0.1997 + 1.0557 0.1997 + 2.1004 0.1997 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. @@ -16148,15 +18700,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.8954 +Replicate 1 : -210.2289 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.485 4.605 0.214 4.763 8.462 1 0.243 0.335 0.212 0.210 2.290 0.231 +rep 1: 2.168 4.088 0.1926 3.926 7.381 1 0.240 0.337 0.213 0.210 1.597 0.201 Treelengths: TL -rep 1: 2.447 +rep 1: 2.444 Saving final tree from best search rep (#1) to ch.n.const.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.const.internalstates.log @@ -16365,6 +18917,7 @@ 600 -13371.2064 0.402 0 700 -13371.0755 0.402 0 800 -13370.9489 0.402 0 +900 -13370.7802 0.402 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16487,15 +19040,15 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 857, seed 144993316, best lnL -13370.870 +Bootstrap rep 1 (of 1) generation 934, seed 1200309585, best lnL -13370.743 gen current_lnL precision last_tree_imp -857 -13370.8704 0.402 0 -900 -13370.7802 0.402 0 +934 -13370.7426 0.402 0 1000 -13370.6791 0.402 0 Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL 1100 -13370.5869 0.304 0 +1200 -13370.5241 0.304 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16505,7 +19058,7 @@ User specified matrix type: ( 0 1 2 2 3 4 ) AC = 1.598, AG = 2.495, AT = 1.210, CG = 1.210, CT = 4.135, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3110 0.1818 0.3061 0.2010 + (ACGT) 0.3079 0.1814 0.3083 0.2024 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.3640 @@ -16522,7 +19075,7 @@ User specified matrix type: ( 0 1 2 1 0 3 ) AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2791 0.1777 0.1601 0.3830 + (ACGT) 0.2812 0.1772 0.1597 0.3819 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 0.2460 @@ -16568,17 +19121,17 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5379 (TERMINATED PREMATURELY) +Replicate 1 : -13370.5104 (TERMINATED PREMATURELY) Parameter estimates: Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 1.598 2.495 1.21 1.21 4.135 1 0.311 0.182 0.306 0.201 0.364 +rep 1: 1.598 2.495 1.21 1.21 4.135 1 0.308 0.181 0.308 0.202 0.364 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.279 0.178 0.160 0.383 0.246 +rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.281 0.177 0.160 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv @@ -16807,7 +19360,7 @@ pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6783 -Time used so far = 0 hours, 0 minutes and 5 seconds +Time used so far = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -16889,6 +19442,8 @@ 400 -467.7465 0.010 0 500 -467.7420 0.010 0 600 -467.7392 0.010 0 +700 -467.7357 0.010 0 +800 -467.7327 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17014,11 +19569,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 636, seed 870003857, best lnL -467.739 +Search rep 2 (of 5) generation 842, seed 2100532500, best lnL -467.731 gen current_lnL precision last_tree_imp -636 -467.7388 0.010 0 -700 -467.7357 0.010 0 -800 -467.7327 0.010 0 +842 -467.7314 0.010 0 900 -467.7314 0.010 0 1000 -467.7285 0.010 0 1100 -467.7270 0.010 0 @@ -17076,7 +19629,7 @@ pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -467.6782 -Time used so far = 0 hours, 0 minutes and 11 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17154,25 +19707,31 @@ 0 -467.8211 0.010 0 100 -467.7944 0.010 0 200 -467.7838 0.010 0 +300 -467.7681 0.010 0 +400 -467.7553 0.010 0 +500 -467.7484 0.010 0 +600 -467.7438 0.010 0 +700 -467.7411 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7743 +Current score = -467.7411 Performing final optimizations... -pass 1 : -467.7688 (branch= 0.0055 subset rates= 0.0000) -pass 2 : -467.7330 (branch= 0.0358 subset rates= 0.0000) -pass 3 : -467.7016 (branch= 0.0313 subset rates= 0.0001) -pass 4 : -467.6877 (branch= 0.0139 subset rates= 0.0000) -pass 5 : -467.6835 (branch= 0.0043 subset rates= 0.0000) -pass 6 : -467.6812 (branch= 0.0023 subset rates= 0.0000) -pass 7 : -467.6802 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -467.6796 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6792 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6790 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6789 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6789 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6788 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6786 (branch= 0.0000 subset rates= 0.0003) +pass 1 : -467.7411 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7086 (branch= 0.0326 subset rates= 0.0000) +pass 3 : -467.7000 (branch= 0.0086 subset rates= 0.0000) +pass 4 : -467.6927 (branch= 0.0074 subset rates= 0.0000) +pass 5 : -467.6857 (branch= 0.0069 subset rates= 0.0000) +pass 6 : -467.6834 (branch= 0.0024 subset rates= 0.0000) +pass 7 : -467.6812 (branch= 0.0018 subset rates= 0.0004) +pass 8 : -467.6801 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -467.6795 (branch= 0.0006 subset rates= 0.0000) +pass 10: -467.6794 (branch= 0.0001 subset rates= 0.0000) +pass 11: -467.6792 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6792 (branch= 0.0000 subset rates= 0.0000) +pass 13: -467.6792 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6791 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6787 (branch= 0.0000 subset rates= 0.0005) Looking for minimum length branches... -Final score = -467.6786 +Final score = -467.6785 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17201,7 +19760,7 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.18 + 0.79 1.47 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. @@ -17220,7 +19779,7 @@ Results: Replicate 1 : -467.6783 Replicate 2 : -467.6782 (best) (same topology as 1) -Replicate 3 : -467.6786 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6785 (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17237,7 +19796,7 @@ TL R(1) R(2) R(3) rep 1: 3.842 0.787 1.477 2.177 rep 2: 3.842 0.787 1.477 2.183 -rep 3: 3.845 0.785 1.485 2.179 +rep 3: 3.844 0.787 1.473 2.190 Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### @@ -17540,6 +20099,9 @@ 400 -477.7283 0.010 102 500 -477.7219 0.010 102 600 -477.7108 0.010 102 +700 -477.7083 0.010 102 +800 -477.6969 0.010 102 +900 -477.6932 0.010 102 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17665,12 +20227,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 699, seed 1629445076, best lnL -477.708 +Search rep 2 (of 5) generation 957, seed 1670414175, best lnL -477.693 gen current_lnL precision last_tree_imp -699 -477.7083 0.010 102 -700 -477.7083 0.010 102 -800 -477.6969 0.010 102 -900 -477.6932 0.010 102 +957 -477.6929 0.010 102 1000 -477.6927 0.010 102 1100 -477.6887 0.010 102 1200 -477.6872 0.010 102 @@ -17711,27 +20270,34 @@ 4700 -477.4710 0.010 2588 4800 -477.4693 0.010 2588 4900 -477.4685 0.010 2588 +5000 -477.4682 0.010 2588 + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL +5100 -477.4677 0.010 2588 +5200 -477.4673 0.010 2588 +5300 -477.4672 0.010 2588 +5400 -477.4670 0.010 2588 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4684 +Current score = -477.4670 Performing final optimizations... -pass 1 : -477.4593 (branch= 0.0055 subset rates= 0.0035) -pass 2 : -477.4548 (branch= 0.0027 subset rates= 0.0018) -pass 3 : -477.4433 (branch= 0.0110 subset rates= 0.0005) -pass 4 : -477.4396 (branch= 0.0037 subset rates= 0.0000) -pass 5 : -477.4363 (branch= 0.0033 subset rates= 0.0000) -pass 6 : -477.4343 (branch= 0.0017 subset rates= 0.0003) -pass 7 : -477.4334 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -477.4328 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -477.4323 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4321 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4320 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4319 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4319 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4319 (branch= 0.0000 subset rates= 0.0000) -pass 15: -477.4319 (branch= 0.0000 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0003) +pass 1 : -477.4601 (branch= 0.0055 subset rates= 0.0014) +pass 2 : -477.4513 (branch= 0.0052 subset rates= 0.0036) +pass 3 : -477.4416 (branch= 0.0098 subset rates= 0.0000) +pass 4 : -477.4383 (branch= 0.0022 subset rates= 0.0011) +pass 5 : -477.4360 (branch= 0.0023 subset rates= 0.0000) +pass 6 : -477.4350 (branch= 0.0010 subset rates= 0.0000) +pass 7 : -477.4336 (branch= 0.0012 subset rates= 0.0001) +pass 8 : -477.4330 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -477.4325 (branch= 0.0005 subset rates= 0.0000) +pass 10: -477.4319 (branch= 0.0003 subset rates= 0.0004) +pass 11: -477.4317 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0000) +pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4316 +Final score = -477.4315 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17778,7 +20344,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -477.4317 -Replicate 2 : -477.4316 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 2 : -477.4315 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17794,7 +20360,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.928 0.632 1.918 2.729 -rep 2: 4.929 0.631 1.914 2.744 +rep 2: 4.928 0.632 1.914 2.739 Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18080,6 +20646,7 @@ gen current_lnL precision last_tree_imp 0 -439.2274 0.010 0 100 -428.8675 0.010 98 +200 -428.0498 0.010 164 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18208,10 +20775,9 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 181, seed 1318331368, best lnL -428.094 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 288, seed 619412858, best lnL -427.600 gen current_lnL precision last_tree_imp -181 -428.0941 0.010 164 -200 -428.0498 0.010 164 +288 -427.6002 0.010 249 300 -427.6002 0.010 249 400 -427.5647 0.010 249 500 -427.4910 0.010 499 @@ -18267,7 +20833,7 @@ pass 14: -425.5489 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5489 -Time used so far = 0 hours, 0 minutes and 11 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18321,24 +20887,28 @@ 400 -427.2439 0.010 295 500 -427.2138 0.010 295 600 -427.1679 0.010 568 +700 -427.1487 0.010 568 +800 -425.4818 0.010 762 +900 -425.4264 0.010 803 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -427.1628 +Current score = -425.4264 Performing final optimizations... -pass 1 : -427.1323 (branch= 0.0234 subset rates= 0.0071) -pass 2 : -427.0802 (branch= 0.0521 subset rates= 0.0000) -pass 3 : -427.0632 (branch= 0.0170 subset rates= 0.0000) -pass 4 : -427.0543 (branch= 0.0087 subset rates= 0.0001) -pass 5 : -427.0510 (branch= 0.0034 subset rates= 0.0000) -pass 6 : -427.0499 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -427.0496 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -427.0493 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -427.0492 (branch= 0.0001 subset rates= 0.0000) -pass 10: -427.0491 (branch= 0.0000 subset rates= 0.0000) -pass 11: -427.0491 (branch= 0.0000 subset rates= 0.0000) -pass 12: -427.0491 (branch= 0.0000 subset rates= 0.0000) -pass 13: -427.0491 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3928 (branch= 0.0318 subset rates= 0.0017) +pass 2 : -425.3612 (branch= 0.0278 subset rates= 0.0038) +pass 3 : -425.3300 (branch= 0.0312 subset rates= 0.0000) +pass 4 : -425.3230 (branch= 0.0069 subset rates= 0.0000) +pass 5 : -425.3221 (branch= 0.0009 subset rates= 0.0000) +pass 6 : -425.3217 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -425.3212 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -425.3210 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -425.3209 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3208 (branch= 0.0001 subset rates= 0.0000) +pass 11: -425.3208 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3208 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.3208 (branch= 0.0000 subset rates= 0.0000) +pass 14: -425.3208 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -427.0490 +Final score = -425.3208 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18367,9 +20937,9 @@ no rate heterogeneity Subset rate multipliers: - 0.88 1.48 1.10 + 0.87 1.53 1.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 10 branches were collapsed. >>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< @@ -18385,8 +20955,8 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5495 -Replicate 2 : -425.5489 (best) -Replicate 3 : -427.0490 (TERMINATED PREMATURELY) +Replicate 2 : -425.5489 +Replicate 3 : -425.3208 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18403,10 +20973,11 @@ TL R(1) R(2) R(3) rep 1: 3.035 0.865 1.541 1.123 rep 2: 3.040 0.869 1.529 1.111 -rep 3: 3.178 0.881 1.482 1.096 +rep 3: 2.983 0.867 1.531 1.144 -Saving tree from best search rep (#2) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -18824,9 +21395,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 51, seed 904888451, best lnL -474.792 +Search rep 2 (of 5) generation 28, seed 83845019, best lnL -474.799 gen current_lnL precision last_tree_imp -51 -474.7919 0.010 0 +28 -474.7991 0.010 0 100 -474.7908 0.010 0 200 -474.7012 0.010 123 300 -474.5326 0.010 272 @@ -18865,23 +21436,24 @@ 3600 -474.4594 0.010 272 3700 -474.4590 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4590 +Current score = -474.4584 Performing final optimizations... -pass 1 : -474.4542 (branch= 0.0048 subset rates= 0.0000) -pass 2 : -474.4435 (branch= 0.0108 subset rates= 0.0000) -pass 3 : -474.4372 (branch= 0.0063 subset rates= 0.0000) -pass 4 : -474.4345 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -474.4330 (branch= 0.0015 subset rates= 0.0000) -pass 6 : -474.4309 (branch= 0.0018 subset rates= 0.0002) -pass 7 : -474.4299 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -474.4291 (branch= 0.0008 subset rates= 0.0000) +pass 1 : -474.4536 (branch= 0.0048 subset rates= 0.0000) +pass 2 : -474.4429 (branch= 0.0107 subset rates= 0.0000) +pass 3 : -474.4366 (branch= 0.0063 subset rates= 0.0000) +pass 4 : -474.4340 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -474.4331 (branch= 0.0009 subset rates= 0.0000) +pass 6 : -474.4312 (branch= 0.0018 subset rates= 0.0000) +pass 7 : -474.4303 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -474.4291 (branch= 0.0008 subset rates= 0.0005) pass 9 : -474.4286 (branch= 0.0005 subset rates= 0.0000) -pass 10: -474.4283 (branch= 0.0003 subset rates= 0.0000) -pass 11: -474.4282 (branch= 0.0001 subset rates= 0.0000) -pass 12: -474.4282 (branch= 0.0001 subset rates= 0.0000) -pass 13: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 10: -474.4284 (branch= 0.0002 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4282 (branch= 0.0000 subset rates= 0.0001) +pass 13: -474.4282 (branch= 0.0001 subset rates= 0.0000) pass 14: -474.4281 (branch= 0.0000 subset rates= 0.0000) pass 15: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 16: -474.4281 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -474.4281 Time used so far = 0 hours, 0 minutes and 12 seconds @@ -18912,7 +21484,7 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.92 + 0.59 2.03 2.93 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. @@ -18946,7 +21518,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.348 0.589 2.066 2.793 -rep 2: 4.601 0.587 2.033 2.924 +rep 2: 4.601 0.587 2.032 2.926 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -19013,10 +21585,10 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_arm64.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_arm64.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-deb: building package 'garli' in '../garli_2.1-7_arm64.deb'. +dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_arm64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_arm64.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_arm64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_arm64.changes @@ -19025,12 +21597,14 @@ 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/15721/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/15721/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/11142 and its subdirectories -I: Current time: Fri Apr 28 21:09:04 -12 2023 -I: pbuilder-time-stamp: 1682759344 +I: removing directory /srv/workspace/pbuilder/15721 and its subdirectories +I: Current time: Sat Jun 1 05:48:18 +14 2024 +I: pbuilder-time-stamp: 1717170498