Diff of the two buildlogs: -- --- b1/build.log 2023-05-05 04:40:10.987791587 +0000 +++ b2/build.log 2023-05-05 04:59:52.627923384 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu May 4 16:26:56 -12 2023 -I: pbuilder-time-stamp: 1683260816 +I: Current time: Fri May 5 18:41:26 +14 2023 +I: pbuilder-time-stamp: 1683261686 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ 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 @@ -25,135 +25,167 @@ 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/32726/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/28897/tmp/hooks/D01_modify_environment starting +debug: Running on virt32a. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 5 18:43 /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/28897/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/28897/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='a9fb300977a04cb8aeb73fa4d471fed5' - 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='32726' - PS1='# ' - PS2='> ' + INVOCATION_ID=50b26036450041818339daff68553170 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=28897 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.q427glx6/pbuilderrc_yWBT --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.q427glx6/b1 --logfile b1/build.log garli_2.1-7.dsc' - SUDO_GID='114' - SUDO_UID='108' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.q427glx6/pbuilderrc_7rMj --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.q427glx6/b2 --logfile b2/build.log --extrapackages usrmerge garli_2.1-7.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux jtx1a 5.10.0-22-arm64 #1 SMP Debian 5.10.178-3 (2023-04-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-armmp-lpae #1 SMP Debian 5.10.178-3 (2023-04-22) armv7l GNU/Linux I: ls -l /bin total 5072 - -rwxr-xr-x 1 root root 838488 Apr 23 09:24 bash - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 67144 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 67112 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 67632 Sep 20 2022 cat - -rwxr-xr-x 1 root root 67676 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 67644 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 67684 Sep 20 2022 chown - -rwxr-xr-x 1 root root 133532 Sep 20 2022 cp - -rwxr-xr-x 1 root root 132868 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 133220 Sep 20 2022 date - -rwxr-xr-x 1 root root 67732 Sep 20 2022 dd - -rwxr-xr-x 1 root root 68104 Sep 20 2022 df - -rwxr-xr-x 1 root root 133632 Sep 20 2022 dir - -rwxr-xr-x 1 root root 59128 Mar 22 21:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 67560 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 67548 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 55748 Mar 22 21:02 findmnt - -rwsr-xr-x 1 root root 26208 Mar 22 20:15 fusermount - -rwxr-xr-x 1 root root 128608 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 64220 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 67032 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 67720 Sep 20 2022 ln - -rwxr-xr-x 1 root root 35132 Mar 22 21:51 login - -rwxr-xr-x 1 root root 133632 Sep 20 2022 ls - -rwxr-xr-x 1 root root 136808 Mar 22 21:02 lsblk - -rwxr-xr-x 1 root root 67800 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 67764 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 67596 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 38504 Mar 22 21:02 more - -rwsr-xr-x 1 root root 38496 Mar 22 21:02 mount - -rwxr-xr-x 1 root root 9824 Mar 22 21:02 mountpoint - -rwxr-xr-x 1 root root 133532 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 67608 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:24 rbash -> bash - -rwxr-xr-x 1 root root 67600 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 67672 Sep 20 2022 rm - -rwxr-xr-x 1 root root 67600 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 67400 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 133372 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 67644 Sep 20 2022 stty - -rwsr-xr-x 1 root root 50800 Mar 22 21:02 su - -rwxr-xr-x 1 root root 67584 Sep 20 2022 sync - -rwxr-xr-x 1 root root 336764 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 67144 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 133224 Sep 20 2022 touch - -rwxr-xr-x 1 root root 67548 Sep 20 2022 true - -rwxr-xr-x 1 root root 9768 Mar 22 20:15 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Mar 22 21:02 umount - -rwxr-xr-x 1 root root 67572 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 133632 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 42608 Mar 22 21:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/32726/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 67144 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 67112 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 67632 Sep 21 2022 cat + -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown + -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp + -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 133220 Sep 21 2022 date + -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd + -rwxr-xr-x 1 root root 68104 Sep 21 2022 df + -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir + -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname + -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 67548 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt + -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount + -rwxr-xr-x 1 root root 128608 Jan 25 04:43 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 64220 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln + -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login + -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls + -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk + -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more + -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount + -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint + -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash + -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm + -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 5 18:43 sh -> /bin/bash + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty + -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su + -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync + -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch + -rwxr-xr-x 1 root root 67548 Sep 21 2022 true + -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount + -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/28897/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -282,7 +314,7 @@ Get: 83 http://deb.debian.org/debian bookworm/main armhf openmpi-bin armhf 4.1.4-3+b1 [194 kB] Get: 84 http://deb.debian.org/debian bookworm/main armhf libopenmpi-dev armhf 4.1.4-3+b1 [920 kB] Get: 85 http://deb.debian.org/debian bookworm/main armhf ncl-tools armhf 2.1.21+git20210811.b1213a7-4 [138 kB] -Fetched 39.1 MB in 3s (11.2 MB/s) +Fetched 39.1 MB in 1s (34.1 MB/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 ... 19329 files and directories currently installed.) @@ -639,8 +671,19 @@ 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/28897/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/28897/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +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 @@ -737,13 +780,13 @@ checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no 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 @@ -774,8 +817,8 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes @@ -812,7 +855,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j3 + make -j4 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -821,6 +864,29 @@ 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 adaptation.o adaptation.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 bipartition.o bipartition.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 condlike.o condlike.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 configoptions.o configoptions.cpp +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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/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{ @@ -865,6 +931,23 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +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); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 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 configreader.o configreader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -921,53 +1004,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/ncl/ncl.h:27, + from garlireader.cpp:41: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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 model.o model.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 optimization.o optimization.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 population.o population.cpp In file included from /usr/include/c++/12/vector:63, from /usr/include/ncl/ncl.h:60: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': @@ -1468,26 +1532,6 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from population.h:24: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __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 linalg.o linalg.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -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 model.o model.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 optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -1538,7 +1582,6 @@ /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 population.o population.cpp In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -1584,50 +1627,6 @@ /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){ - | ^ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1675,11 +1674,85 @@ /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){ + | ^ +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 +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 sequencedata.o sequencedata.cpp +population.cpp: In member function 'void Population::RunTests()': +population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ +reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': +reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 388 | fread(&unique, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +reconnode.h: In constructor 'Swap::Swap(FILE*&)': +reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 264 | fread(&count, scalarSize, 1, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from treenode.h:30, + from tree.h:31: +bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': +bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': +population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1880 | fread((char *) &seed, sizeof(seed), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1887 | fread((char *) &t, sizeof(t), 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] + 1896 | fread(this, scalarSize, 1, pin); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -1719,34 +1792,6 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -population.cpp: In member function 'void Population::RunTests()': -population.cpp:875:46: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ -reconnode.h: In member function 'void AttemptedSwapList::ReadBinarySwapCheckpoint(FILE*&)': -reconnode.h:388:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 388 | fread(&unique, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -reconnode.h: In constructor 'Swap::Swap(FILE*&)': -reconnode.h:264:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 264 | fread(&count, scalarSize, 1, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from treenode.h:30, - from tree.h:31: -bipartition.h: In member function 'void Bipartition::BinaryInput(FILE*&)': -bipartition.h:518:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 518 | fread((char*) rep, sizeof(unsigned int), nBlocks, in); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp: In member function 'void Population::ReadPopulationCheckpoint()': -population.cpp:1880:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1880 | fread((char *) &seed, sizeof(seed), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1887:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1887 | fread((char *) &t, sizeof(t), 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1896 | fread(this, scalarSize, 1, pin); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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, @@ -1780,6 +1825,27 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 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 +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 datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from /usr/include/c++/12/vector:70, from model.h:28, from model.cpp:25: @@ -1793,7 +1859,11 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __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 rng.o rng.cpp +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4957:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -1805,12 +1875,19 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -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 +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -1833,19 +1910,6 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4894:19: @@ -1870,6 +1934,7 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'InsertProportion::InsertProportion(FLOAT_TYPE**, int)' at model.h:340:149, @@ -1926,100 +1991,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, - inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'void Population::OptimizeSiteRates()' at population.cpp:7958:21: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -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 -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __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 tree.o tree.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 treenode.o treenode.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2072,11 +2043,50 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, + inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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){ | ^ -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 mpitrick.o mpitrick.cpp +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'void Population::OptimizeSiteRates()' at population.cpp:7958:21: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -2144,17 +2154,47 @@ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 +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 mpitrick.o mpitrick.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __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 treenode.cpp:21: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2225,9 +2265,12 @@ 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 datamatr.h:23, - from sequencedata.h:27, - from tree.cpp:31: + 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 treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -2328,13 +2371,13 @@ checking target system type... arm-unknown-linux-gnueabihf checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes -checking for a race-free mkdir -p... /bin/mkdir -p +checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no 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 @@ -2365,8 +2408,8 @@ checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes -checking for grep that handles long lines and -e... /bin/grep -checking for egrep... /bin/grep -E +checking for grep that handles long lines and -e... /usr/bin/grep +checking for egrep... /usr/bin/grep -E checking for float.h... yes checking for malloc.h... yes checking for stddef.h... yes @@ -2401,7 +2444,7 @@ config.status: executing depfiles commands make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j3 + make -j4 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -2410,6 +2453,29 @@ 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 adaptation.o adaptation.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 bipartition.o bipartition.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 condlike.o condlike.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 configoptions.o configoptions.cpp +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/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/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{ @@ -2454,6 +2520,23 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +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); + | ^~ +configoptions.cpp:337:34: note: directive argument in the range [0, 2147483647] + 337 | sprintf(modName, "model%d", modelNum); + | ^~~~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)' at configoptions.cpp:337:10: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +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 configreader.o configreader.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -2510,7 +2593,7 @@ funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/stdio.h:906, + from /usr/include/c++/12/cstdio:42, + from /usr/include/ncl/ncl.h:27, + from garlireader.cpp:41: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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 model.o model.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 optimization.o optimization.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 population.o population.cpp In file included from /usr/include/c++/12/vector:63, from /usr/include/ncl/ncl.h:60: /usr/include/c++/12/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = ProcessedNxsToken*]': @@ -3025,26 +3089,6 @@ /usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70, - from population.h:24: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)' at individual.cpp:755:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __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 linalg.o linalg.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 model.o model.cpp -linalg.cpp: In function 'void CalcPij(const MODEL_FLOAT*, int, const MODEL_FLOAT*, MODEL_FLOAT, MODEL_FLOAT, MODEL_FLOAT**, MODEL_FLOAT*)': -linalg.cpp:1322:33: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 1322 | register int nsq = n * n; - | ^~~ -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 optimization.o optimization.cpp In file included from tree.h:35, from individual.h:21, from model.cpp:26: @@ -3095,7 +3139,6 @@ /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 population.o population.cpp In file included from tree.h:35, from optimization.cpp:19: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] @@ -3150,6 +3193,7 @@ 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 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); @@ -3185,29 +3229,6 @@ 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); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 rng.h:36, - from tree.h:30: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -3260,22 +3281,7 @@ 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 10.1 875 | tree0->CalcDerivativesRateHet(nd->anc, nd); @@ -3304,7 +3310,45 @@ population.cpp:1896:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 1896 | fread(this, scalarSize, 1, pin); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -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 +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 rng.h:36, + from tree.h:30: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] 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, @@ -3322,7 +3366,24 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] -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 +population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': +population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~ +population.cpp:3066:47: note: directive argument in the range [1, 536870911] + 3066 | sprintf(oStr, "R(%d)", d + 1); + | ^~~~~~~ +In function 'int sprintf(char*, const char*, ...)', + inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +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 In file included from /usr/include/c++/12/vector:70, from model.h:28, from model.cpp:25: @@ -3336,22 +3397,37 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': -population.cpp:3066:50: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~ -population.cpp:3066:47: note: directive argument in the range [1, 536870911] - 3066 | sprintf(oStr, "R(%d)", d + 1); - | ^~~~~~~ +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 datamatr.h:23, + from sequencedata.h:27, + from sequencedata.cpp:21: In function 'int sprintf(char*, const char*, ...)', - inlined from 'int Population::EvaluateStoredTrees(bool)' at population.cpp:3066:12: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: '__builtin___sprintf_chk' output between 5 and 13 bytes into a destination of size 10 + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +In file included from /usr/include/c++/12/vector:70: +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/vector:64: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)' at model.cpp:4957:19: /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -3363,15 +3439,17 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, + inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __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 tree.o tree.cpp /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:70: -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::ReadGarliFormattedModelString(std::string&)' at model.cpp:2801:16: @@ -3390,19 +3468,54 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/vector:64: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Population::BetterFinalOptimization()' at population.cpp:2541:30: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Tree::StoreBranchlengths(std::vector&)' at tree.h:313:20, - inlined from 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)' at population.cpp:1449:33: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from funcs.h:25, + from tree.cpp:33: +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.cpp:21: +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 65 | class DistEqualsWithinCutSubtree:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 72 | class NodeEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here + 131 | struct binary_function + | ^~~~~~~~~~~~~~~ +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)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_function.h:1438: +/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::GetFirstNodeAtDistWithinCutSubtree(int)': +reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); + | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/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 member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void ModelPartition::ReadGarliFormattedModelStrings(std::string&)' at model.cpp:4894:19: @@ -3415,25 +3528,10 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __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 datamatr.h:23, - from sequencedata.h:27, - from sequencedata.cpp:21: -In function 'int sprintf(char*, const char*, ...)', - inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: -/usr/include/arm-linux-gnueabihf/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/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, inlined from 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)' at model.cpp:712:20: @@ -3446,6 +3544,10 @@ /usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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 member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, inlined from 'InsertProportion::InsertProportion(FLOAT_TYPE**, int)' at model.h:340:149, @@ -3502,39 +3604,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, - inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 /usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 439 | vector<_Tp, _Alloc>:: @@ -3544,96 +3613,6 @@ /usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1287 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 439 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: -/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: -/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1287 | _M_realloc_insert(end(), __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 tree.o tree.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 treenode.o treenode.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 mpitrick.o mpitrick.cpp -In file included from tree.h:35, - from individual.h:21, - from population.h:31, - from funcs.h:25, - from tree.cpp:33: -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.cpp:21: -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 65 | class DistEqualsWithinCutSubtree:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -reconnode.h:72:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 72 | class NodeEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here - 131 | struct binary_function - | ^~~~~~~~~~~~~~~ -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)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_function.h:1438: -/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::GetFirstNodeAtDistWithinCutSubtree(int)': -reconnode.h:102:57: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = DistEqualsWithinCutSubtree; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 102 | return find_if(l.begin(),l.end(),bind2nd(DistEqualsWithinCutSubtree(), Dist)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/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) - | ^~~~~~~ -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::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){ - | ^ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6808 | fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -3701,17 +3680,77 @@ tree.cpp:6881:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 6881 | fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 439 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +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 treenode.o treenode.cpp +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4686:25: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4687:31: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)' at model.h:109:26, + inlined from 'SubsetRates::SubsetRates(FLOAT_TYPE**, int, int)' at model.h:352:144, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4699:71: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4705:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'ModelPartition::ModelPartition()' at model.cpp:4706:30: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3846:17: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3887:24: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3897:52: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/12/bits/stl_vector.h:1294:21, + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3902:35: +/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void Population::VariableStartingTreeOptimization(bool)' at population.cpp:3906:52: +/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1287 | _M_realloc_insert(end(), __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 treenode.cpp:21: + from datamatr.h:23, + from sequencedata.h:27, + from tree.cpp:31: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3723,14 +3762,18 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: null destination pointer [-Wformat-overflow=] +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 mpitrick.o mpitrick.cpp 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 datamatr.h:23, - from sequencedata.h:27, - from tree.cpp:31: + 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 treenode.cpp:21: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/arm-linux-gnueabihf/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3778,7 +3821,7 @@ # get (mostly!) reproducible test results and avoid failures as described in bug #907905 find tests -name "*.conf" -exec sed -i~ 's/randseed *= *-1/randseed = 1\nbootstrapseed = 42/' \{\} \; dh_auto_test - make -j3 check "TESTSUITEFLAGS=-j3 --verbose" VERBOSE=1 + make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -6298,7 +6341,7 @@ pass 13: -6242.8580 (branch= 0.0000 alpha= 0.0000) Looking for minimum length branches... Final score = -6242.8580 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6448,7 +6491,7 @@ 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 2 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6591,7 +6634,7 @@ pass 11: -6434.5092 (branch= 0.0000) Looking for minimum length branches... Final score = -6434.5092 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6745,7 +6788,7 @@ 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 36 seconds +Time used = 0 hours, 0 minutes and 56 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6897,7 +6940,7 @@ 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 26 seconds +Time used = 0 hours, 0 minutes and 32 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7101,7 +7144,7 @@ pass 75: -3350.2332 (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 = -3350.2333 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7309,7 +7352,7 @@ 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 2 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7626,7 +7669,7 @@ pass 10: -13931.0232 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13931.0232 -Time used = 0 hours, 0 minutes and 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7793,7 +7836,7 @@ pass 15: -14498.8853 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8853 -Time used = 0 hours, 0 minutes and 7 seconds +Time used = 0 hours, 0 minutes and 16 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8047,7 +8090,7 @@ pass 34: -13306.2061 (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 = -13306.2061 -Time used = 0 hours, 0 minutes and 10 seconds +Time used = 0 hours, 0 minutes and 13 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -10017,7 +10060,7 @@ pass 494: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10281,7 +10324,7 @@ pass 372: -208.1244 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.1244 -Time used = 0 hours, 0 minutes and 5 seconds +Time used = 0 hours, 0 minutes and 12 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10573,7 +10616,7 @@ pass 488: -208.3584 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3584 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 10 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10864,7 +10907,7 @@ pass 489: -208.3586 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3586 -Time used = 0 hours, 0 minutes and 6 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13572,8 +13615,6 @@ 200 -91.3705 0.500 199 300 -90.7565 0.500 215 400 -90.4959 0.500 215 -500 -90.3850 0.500 215 -600 -90.2906 0.500 215 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13670,9 +13711,11 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 664, seed 1398765731, best lnL -90.230 +Bootstrap rep 1 (of 1) generation 417, seed 1885547922, best lnL -90.491 gen current_lnL precision last_tree_imp -664 -90.2302 0.500 215 +417 -90.4913 0.500 215 +500 -90.3850 0.500 215 +600 -90.2906 0.500 215 700 -90.2169 0.500 215 800 -90.1648 0.500 215 Optimization precision reduced @@ -13848,8 +13891,6 @@ 0 -116.1434 0.500 0 100 -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 @@ -13936,9 +13977,11 @@ STARTING RUN Restarting from checkpoint... - generation 487, seed 147137001, best lnL -111.824 + generation 200, seed 1008112217, best lnL -112.496 gen current_lnL precision last_tree_imp -487 -111.8239 0.500 84 +200 -112.4964 0.500 84 +300 -112.3224 0.500 84 +400 -112.1061 0.500 84 500 -111.8129 0.500 84 600 -111.7788 0.500 84 Optimization precision reduced @@ -14115,20 +14158,6 @@ 200 -112.5462 0.500 160 300 -112.1250 0.500 160 400 -111.8851 0.500 160 -500 -111.7755 0.500 160 -600 -111.6975 0.500 563 -700 -111.6876 0.500 563 -800 -111.6844 0.500 563 -900 -111.6835 0.500 563 -1000 -111.6829 0.500 563 -1100 -111.6827 0.500 563 -Optimization precision reduced - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -1200 -111.6824 0.010 563 -1300 -111.6822 0.010 563 -1400 -111.6821 0.010 563 -1500 -111.6819 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14214,11 +14243,18 @@ STARTING RUN Restarting from checkpoint... - generation 1596, seed 1731679210, best lnL -111.682 + generation 437, seed 787518119, best lnL -111.837 gen current_lnL precision last_tree_imp -1596 -111.6819 0.010 563 +437 -111.8366 0.500 160 +500 -111.7755 0.500 160 +600 -111.6975 0.500 563 +700 -111.6876 0.500 563 +800 -111.6844 0.500 563 +900 -111.6835 0.500 563 +1000 -111.6829 0.500 563 +NOTE: ****Specified generation limit (1000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -14235,23 +14271,30 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.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 : -111.6819 +Replicate 1 : -111.6829 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.606 +rep 1: 2.616 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 +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf @@ -14375,7 +14418,6 @@ gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 10 -207.1401 0.500 10 -20 -205.6892 0.500 18 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14462,9 +14504,10 @@ STARTING RUN Restarting from checkpoint... - generation 29, seed 2029909503, best lnL -205.650 + generation 10, seed 1509658266, best lnL -207.140 gen current_lnL precision last_tree_imp -29 -205.6499 0.500 18 +10 -207.1401 0.500 10 +20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 50 -205.6175 0.500 18 @@ -14658,7 +14701,6 @@ gen current_lnL precision last_tree_imp 0 -195.4001 0.500 0 10 -195.3555 0.500 0 -20 -195.3342 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14746,9 +14788,10 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 21, seed 950885006, best lnL -195.296 +Bootstrap rep 1 (of 1) generation 10, seed 1509658266, best lnL -195.355 gen current_lnL precision last_tree_imp -21 -195.2958 0.500 0 +10 -195.3555 0.500 0 +20 -195.3342 0.500 0 30 -195.2777 0.500 0 40 -195.2556 0.500 0 50 -195.2139 0.500 0 @@ -14954,27 +14997,6 @@ gen current_lnL precision last_tree_imp 0 -3358.3708 0.500 0 100 -3357.1202 0.500 0 -200 -3356.8081 0.500 0 -300 -3356.5910 0.500 0 -400 -3355.9752 0.500 0 -500 -3355.8101 0.500 0 -Optimization precision reduced - Optimizing parameters... improved 0.940 lnL - Optimizing branchlengths... improved 0.000 lnL -600 -3354.6612 0.255 0 -700 -3354.3974 0.255 0 -800 -3354.0880 0.255 0 -900 -3353.8938 0.255 0 -1000 -3353.6942 0.255 0 -Optimization precision reduced - Optimizing parameters... improved 0.833 lnL - Optimizing branchlengths... improved 0.085 lnL -1100 -3352.7168 0.010 0 -1200 -3352.6373 0.010 0 -1300 -3352.5144 0.010 0 -1400 -3352.4046 0.010 0 -1500 -3352.3996 0.010 0 -1600 -3352.2933 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15078,79 +15100,85 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1623, seed 1001019763, best lnL -3352.293 +Search rep 1 (of 2) generation 100, seed 1637930417, best lnL -3357.120 gen current_lnL precision last_tree_imp -1623 -3352.2933 0.010 0 -1700 -3352.2857 0.010 0 -1800 -3352.2040 0.010 0 -1900 -3351.8438 0.010 0 -2000 -3351.7704 0.010 0 -2100 -3351.6146 0.010 0 -2200 -3351.3691 0.010 0 -2300 -3351.3430 0.010 0 -2400 -3351.3354 0.010 0 -2500 -3351.2335 0.010 0 -2600 -3351.1680 0.010 0 -2700 -3351.1678 0.010 0 -2800 -3351.1163 0.010 0 -2900 -3351.1148 0.010 0 -3000 -3351.1107 0.010 0 +100 -3357.1202 0.500 0 +200 -3356.8081 0.500 0 +300 -3356.5910 0.500 0 +400 -3355.9752 0.500 0 +500 -3355.8101 0.500 0 +Optimization precision reduced + Optimizing parameters... improved 0.940 lnL + Optimizing branchlengths... improved 0.000 lnL +600 -3354.6612 0.255 0 +700 -3354.3974 0.255 0 +800 -3354.0880 0.255 0 +900 -3353.8938 0.255 0 +1000 -3353.6942 0.255 0 +Optimization precision reduced + Optimizing parameters... improved 0.833 lnL + Optimizing branchlengths... improved 0.085 lnL +1100 -3352.7168 0.010 0 +1200 -3352.6373 0.010 0 +1300 -3352.5144 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3351.1107 +Current score = -3352.5144 Performing final optimizations... -pass 1 : -3351.0504 (branch= 0.0000 alpha= 0.0000 pinv= 0.0227 eq freqs= 0.0001 rel rates= 0.0374 subset rates= 0.0000) -pass 2 : -3350.9515 (branch= 0.0000 alpha= 0.0117 pinv= 0.0195 eq freqs= 0.0100 rel rates= 0.0578 subset rates= 0.0000) -pass 3 : -3350.8639 (branch= 0.0032 alpha= 0.0186 pinv= 0.0171 eq freqs= 0.0020 rel rates= 0.0467 subset rates= 0.0000) -pass 4 : -3350.7872 (branch= 0.0033 alpha= 0.0186 pinv= 0.0153 eq freqs= 0.0000 rel rates= 0.0380 subset rates= 0.0014) -pass 5 : -3350.7193 (branch= 0.0062 alpha= 0.0142 pinv= 0.0147 eq freqs= 0.0010 rel rates= 0.0303 subset rates= 0.0016) -pass 6 : -3350.6611 (branch= 0.0042 alpha= 0.0129 pinv= 0.0137 eq freqs= 0.0002 rel rates= 0.0271 subset rates= 0.0000) -pass 7 : -3350.6090 (branch= 0.0008 alpha= 0.0126 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0240 subset rates= 0.0021) -pass 8 : -3350.5641 (branch= 0.0022 alpha= 0.0116 pinv= 0.0114 eq freqs= 0.0000 rel rates= 0.0196 subset rates= 0.0000) -pass 9 : -3350.5232 (branch= 0.0004 alpha= 0.0105 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0181 subset rates= 0.0014) -pass 10: -3350.4872 (branch= 0.0014 alpha= 0.0097 pinv= 0.0100 eq freqs= 0.0000 rel rates= 0.0148 subset rates= 0.0000) -pass 11: -3350.4563 (branch= 0.0002 alpha= 0.0087 pinv= 0.0085 eq freqs= 0.0000 rel rates= 0.0134 subset rates= 0.0000) -pass 12: -3350.4285 (branch= 0.0000 alpha= 0.0083 pinv= 0.0076 eq freqs= 0.0000 rel rates= 0.0118 subset rates= 0.0000) -pass 13: -3350.4038 (branch= 0.0000 alpha= 0.0076 pinv= 0.0068 eq freqs= 0.0000 rel rates= 0.0102 subset rates= 0.0000) -pass 14: -3350.3810 (branch= 0.0000 alpha= 0.0068 pinv= 0.0061 eq freqs= 0.0000 rel rates= 0.0088 subset rates= 0.0010) -pass 15: -3350.3621 (branch= 0.0006 alpha= 0.0058 pinv= 0.0055 eq freqs= 0.0000 rel rates= 0.0070 subset rates= 0.0000) -pass 16: -3350.3458 (branch= 0.0001 alpha= 0.0051 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0064 subset rates= 0.0000) -pass 17: -3350.3312 (branch= 0.0000 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0056 subset rates= 0.0000) -pass 18: -3350.3181 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0050 subset rates= 0.0000) -pass 19: -3350.3068 (branch= 0.0000 alpha= 0.0038 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) -pass 20: -3350.2969 (branch= 0.0000 alpha= 0.0033 pinv= 0.0030 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2472 (branch= 0.0000 alpha= 0.0167 pinv= 0.0151 eq freqs= 0.0000 rel rates= 0.0178 subset rates= 0.0000) +pass 1 : -3352.1666 (branch= 0.0000 alpha= 0.0000 pinv= 0.0074 eq freqs= 0.0210 rel rates= 0.3194 subset rates= 0.0000) +pass 2 : -3351.8691 (branch= 0.0272 alpha= 0.0119 pinv= 0.0189 eq freqs= 0.0039 rel rates= 0.2289 subset rates= 0.0068) +pass 3 : -3351.6119 (branch= 0.0211 alpha= 0.0138 pinv= 0.0179 eq freqs= 0.0066 rel rates= 0.1923 subset rates= 0.0055) +pass 4 : -3351.4081 (branch= 0.0107 alpha= 0.0126 pinv= 0.0168 eq freqs= 0.0011 rel rates= 0.1592 subset rates= 0.0034) +pass 5 : -3351.2382 (branch= 0.0083 alpha= 0.0130 pinv= 0.0157 eq freqs= 0.0005 rel rates= 0.1296 subset rates= 0.0028) +pass 6 : -3351.0935 (branch= 0.0067 alpha= 0.0126 pinv= 0.0147 eq freqs= 0.0006 rel rates= 0.1078 subset rates= 0.0023) +pass 7 : -3350.9671 (branch= 0.0053 alpha= 0.0112 pinv= 0.0136 eq freqs= 0.0006 rel rates= 0.0942 subset rates= 0.0015) +pass 8 : -3350.8624 (branch= 0.0034 alpha= 0.0112 pinv= 0.0126 eq freqs= 0.0002 rel rates= 0.0774 subset rates= 0.0000) +pass 9 : -3350.7716 (branch= 0.0008 alpha= 0.0112 pinv= 0.0115 eq freqs= 0.0002 rel rates= 0.0655 subset rates= 0.0017) +pass 10: -3350.6956 (branch= 0.0013 alpha= 0.0108 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0523 subset rates= 0.0000) +pass 11: -3350.6308 (branch= 0.0004 alpha= 0.0097 pinv= 0.0101 eq freqs= 0.0001 rel rates= 0.0446 subset rates= 0.0000) +pass 12: -3350.5735 (branch= 0.0001 alpha= 0.0094 pinv= 0.0091 eq freqs= 0.0001 rel rates= 0.0373 subset rates= 0.0012) +pass 13: -3350.5278 (branch= 0.0006 alpha= 0.0083 pinv= 0.0077 eq freqs= 0.0002 rel rates= 0.0289 subset rates= 0.0000) +pass 14: -3350.4884 (branch= 0.0001 alpha= 0.0073 pinv= 0.0070 eq freqs= 0.0000 rel rates= 0.0249 subset rates= 0.0000) +pass 15: -3350.4541 (branch= 0.0000 alpha= 0.0068 pinv= 0.0062 eq freqs= 0.0000 rel rates= 0.0212 subset rates= 0.0000) +pass 16: -3350.4242 (branch= 0.0000 alpha= 0.0062 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0180 subset rates= 0.0000) +pass 17: -3350.3984 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0153 subset rates= 0.0000) +pass 18: -3350.3760 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0130 subset rates= 0.0000) +pass 19: -3350.3567 (branch= 0.0000 alpha= 0.0044 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0110 subset rates= 0.0000) +pass 20: -3350.3400 (branch= 0.0000 alpha= 0.0039 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0094 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2577 (branch= 0.0000 alpha= 0.0198 pinv= 0.0180 eq freqs= 0.0001 rel rates= 0.0444 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2389 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0102 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2360 (branch= 0.0000 alpha= 0.0037 pinv= 0.0034 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) +pass 50: -3350.2346 (branch= 0.0000 alpha= 0.0009 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0026 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2336 (branch= 0.0000 alpha= 0.0007 pinv= 0.0006 eq freqs= 0.0000 rel rates= 0.0011 subset rates= 0.0000) +pass 60: -3350.2337 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... -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) +pass 70: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) optimization up to ... -pass 69: -3350.2330 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 71: -3350.2335 (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 = -3350.2331 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3350.2335 +Time used so far = 0 hours, 0 minutes and 17 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.115, AG = 10.419, AT = 2.691, CG = 0.001, CT = 21.942, GT = 1.000 + AC = 3.111, AG = 10.397, AT = 2.685, CG = 0.001, CT = 21.859, 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 - 0.5773 + 0.5787 with an invariant (invariable) site category, proportion estimated - 0.3657 + 0.3661 Substitution rate categories under this model: rate proportion - 0.0000 0.3657 - 0.0485 0.1586 - 0.2994 0.1586 - 0.8693 0.1586 - 2.7828 0.1586 + 0.0000 0.3661 + 0.0487 0.1585 + 0.3002 0.1585 + 0.8700 0.1585 + 2.7810 0.1585 Model 2 Number of states = 2 (binary data) @@ -15175,20 +15203,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2331 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2335 (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: 3.115 10.42 2.691 0.001 21.94 1 0.333 0.222 0.157 0.288 0.577 0.366 +rep 1: 3.111 10.4 2.685 0.001 21.86 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters Treelengths and subset rate multipliers: TL R(1) R(2) -rep 1: 0.789 1.821 0.179 +rep 1: 0.788 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -15336,9 +15364,6 @@ 0 -3332.4700 0.500 0 100 -3324.9856 0.500 1 200 -3324.7543 0.500 1 -300 -3324.3007 0.500 1 -400 -3323.9848 0.500 1 -500 -3323.6818 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15439,75 +15464,70 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 550, seed 1321880065, best lnL -3323.456 +Search rep 1 (of 2) generation 241, seed 367021991, best lnL -3324.638 gen current_lnL precision last_tree_imp -550 -3323.4558 0.500 1 -600 -3323.3460 0.500 1 -Optimization precision reduced - Optimizing parameters... improved 1.812 lnL - Optimizing branchlengths... improved 0.023 lnL -700 -3321.3650 0.255 1 -800 -3321.0295 0.255 1 -900 -3321.0142 0.255 1 -1000 -3320.9667 0.255 1 +241 -3324.6381 0.500 1 +300 -3324.3007 0.500 1 +400 -3323.9848 0.500 1 +500 -3323.6818 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.8988 +Current score = -3323.3791 Performing final optimizations... -pass 1 : -3320.2618 (branch= 0.0468 alpha= 0.0000 pinv= 0.0155 eq freqs= 0.0001 rel rates= 0.5580 ins/del rates= 0.0166) -pass 2 : -3319.8081 (branch= 0.0688 alpha= 0.0064 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.3444 ins/del rates= 0.0180) -pass 3 : -3319.4760 (branch= 0.0417 alpha= 0.0093 pinv= 0.0157 eq freqs= 0.0000 rel rates= 0.2467 ins/del rates= 0.0187) -pass 4 : -3319.2094 (branch= 0.0263 alpha= 0.0091 pinv= 0.0154 eq freqs= 0.0020 rel rates= 0.2036 ins/del rates= 0.0102) -pass 5 : -3318.9875 (branch= 0.0185 alpha= 0.0103 pinv= 0.0147 eq freqs= 0.0013 rel rates= 0.1695 ins/del rates= 0.0076) -pass 6 : -3318.8026 (branch= 0.0134 alpha= 0.0096 pinv= 0.0138 eq freqs= 0.0013 rel rates= 0.1411 ins/del rates= 0.0057) -pass 7 : -3318.6460 (branch= 0.0086 alpha= 0.0103 pinv= 0.0129 eq freqs= 0.0003 rel rates= 0.1208 ins/del rates= 0.0036) -pass 8 : -3318.5179 (branch= 0.0056 alpha= 0.0100 pinv= 0.0121 eq freqs= 0.0002 rel rates= 0.0978 ins/del rates= 0.0024) -pass 9 : -3318.4102 (branch= 0.0037 alpha= 0.0098 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0811 ins/del rates= 0.0016) -pass 10: -3318.3188 (branch= 0.0024 alpha= 0.0095 pinv= 0.0109 eq freqs= 0.0002 rel rates= 0.0673 ins/del rates= 0.0010) -pass 11: -3318.2440 (branch= 0.0016 alpha= 0.0089 pinv= 0.0094 eq freqs= 0.0002 rel rates= 0.0540 ins/del rates= 0.0007) -pass 12: -3318.1805 (branch= 0.0011 alpha= 0.0083 pinv= 0.0086 eq freqs= 0.0001 rel rates= 0.0449 ins/del rates= 0.0005) -pass 13: -3318.1264 (branch= 0.0007 alpha= 0.0078 pinv= 0.0078 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0003) -pass 14: -3318.0803 (branch= 0.0004 alpha= 0.0073 pinv= 0.0071 eq freqs= 0.0001 rel rates= 0.0309 ins/del rates= 0.0002) -pass 15: -3318.0412 (branch= 0.0003 alpha= 0.0066 pinv= 0.0064 eq freqs= 0.0001 rel rates= 0.0256 ins/del rates= 0.0001) -pass 16: -3318.0076 (branch= 0.0002 alpha= 0.0060 pinv= 0.0058 eq freqs= 0.0001 rel rates= 0.0215 ins/del rates= 0.0001) -pass 17: -3317.9782 (branch= 0.0001 alpha= 0.0054 pinv= 0.0052 eq freqs= 0.0001 rel rates= 0.0185 ins/del rates= 0.0000) -pass 18: -3317.9528 (branch= 0.0001 alpha= 0.0049 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0157 ins/del rates= 0.0000) -pass 19: -3317.9308 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0134 ins/del rates= 0.0000) -pass 20: -3317.9117 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0115 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8164 (branch= 0.0001 alpha= 0.0213 pinv= 0.0196 eq freqs= 0.0001 rel rates= 0.0542 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7937 (branch= 0.0001 alpha= 0.0053 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0124 ins/del rates= 0.0000) +pass 1 : -3321.1625 (branch= 0.0809 alpha= 0.0053 pinv= 0.0162 eq freqs= 0.0760 rel rates= 0.6741 ins/del rates= 1.3641) +pass 2 : -3320.4671 (branch= 0.1141 alpha= 0.0000 pinv= 0.0300 eq freqs= 0.0144 rel rates= 0.5069 ins/del rates= 0.0299) +pass 3 : -3319.9579 (branch= 0.0614 alpha= 0.0048 pinv= 0.0162 eq freqs= 0.0150 rel rates= 0.3871 ins/del rates= 0.0246) +pass 4 : -3319.5645 (branch= 0.0361 alpha= 0.0091 pinv= 0.0153 eq freqs= 0.0039 rel rates= 0.3142 ins/del rates= 0.0147) +pass 5 : -3319.2468 (branch= 0.0239 alpha= 0.0102 pinv= 0.0145 eq freqs= 0.0021 rel rates= 0.2576 ins/del rates= 0.0094) +pass 6 : -3318.9921 (branch= 0.0149 alpha= 0.0098 pinv= 0.0140 eq freqs= 0.0008 rel rates= 0.2091 ins/del rates= 0.0061) +pass 7 : -3318.7934 (branch= 0.0094 alpha= 0.0104 pinv= 0.0131 eq freqs= 0.0008 rel rates= 0.1612 ins/del rates= 0.0039) +pass 8 : -3318.6302 (branch= 0.0060 alpha= 0.0102 pinv= 0.0122 eq freqs= 0.0006 rel rates= 0.1315 ins/del rates= 0.0026) +pass 9 : -3318.4984 (branch= 0.0040 alpha= 0.0099 pinv= 0.0113 eq freqs= 0.0004 rel rates= 0.1045 ins/del rates= 0.0017) +pass 10: -3318.3897 (branch= 0.0026 alpha= 0.0095 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0841 ins/del rates= 0.0011) +pass 11: -3318.3003 (branch= 0.0017 alpha= 0.0090 pinv= 0.0095 eq freqs= 0.0002 rel rates= 0.0681 ins/del rates= 0.0008) +pass 12: -3318.2263 (branch= 0.0011 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0002 rel rates= 0.0550 ins/del rates= 0.0005) +pass 13: -3318.1643 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0450 ins/del rates= 0.0003) +pass 14: -3318.1116 (branch= 0.0005 alpha= 0.0072 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0374 ins/del rates= 0.0002) +pass 15: -3318.0670 (branch= 0.0003 alpha= 0.0068 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0001) +pass 16: -3318.0292 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0001 rel rates= 0.0254 ins/del rates= 0.0001) +pass 17: -3317.9966 (branch= 0.0001 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0001 rel rates= 0.0215 ins/del rates= 0.0000) +pass 18: -3317.9685 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0182 ins/del rates= 0.0000) +pass 19: -3317.9442 (branch= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0155 ins/del rates= 0.0000) +pass 20: -3317.9231 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0132 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8190 (branch= 0.0001 alpha= 0.0217 pinv= 0.0200 eq freqs= 0.0001 rel rates= 0.0622 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7943 (branch= 0.0001 alpha= 0.0054 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7885 (branch= 0.0000 alpha= 0.0011 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0030 ins/del rates= 0.0000) +pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0010 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0007 ins/del rates= 0.0000) +pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0009 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 73: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 74: -3317.7871 (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 = -3317.7871 -Time used so far = 0 hours, 0 minutes and 13 seconds +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.272, AT = 2.658, CG = 0.001, CT = 21.556, GT = 1.000 + AC = 3.066, AG = 10.265, AT = 2.655, CG = 0.001, CT = 21.537, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.3328 0.2223 0.1567 0.2882 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.5746 + 0.5751 with an invariant (invariable) site category, proportion estimated - 0.3612 + 0.3614 Substitution rate categories under this model: rate proportion - 0.0000 0.3612 - 0.0479 0.1597 - 0.2978 0.1597 - 0.8678 0.1597 - 2.7865 0.1597 + 0.0000 0.3614 + 0.0480 0.1596 + 0.2981 0.1596 + 0.8680 0.1596 + 2.7858 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15539,7 +15559,7 @@ 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: 3.067 10.27 2.658 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.066 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15549,7 +15569,7 @@ Treelengths: TL -rep 1: 1.419 +rep 1: 1.418 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -15684,19 +15704,6 @@ 3800 -210.7083 0.010 1104 4000 -210.6946 0.010 1104 4200 -210.6740 0.010 1104 -4400 -210.6492 0.010 1104 -4600 -210.6257 0.010 1104 -4800 -210.5948 0.010 1104 -5000 -210.5740 0.010 1104 -5200 -210.5693 0.010 1104 -5400 -210.5461 0.010 1104 -5600 -210.5133 0.010 1104 -5800 -210.4816 0.010 1104 -6000 -210.4626 0.010 1104 -6200 -210.4591 0.010 1104 -6400 -210.4379 0.010 1104 -6600 -210.4141 0.010 1104 -6800 -210.3876 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15776,93 +15783,57 @@ STARTING RUN Restarting from checkpoint... - generation 6807, seed 343516762, best lnL -210.388 + generation 4205, seed 1340476893, best lnL -210.672 gen current_lnL precision last_tree_imp -6807 -210.3876 0.010 1104 -6900 -210.3335 0.010 1104 -7000 -210.3298 0.010 1104 -7100 -210.3072 0.010 1104 -7200 -210.2823 0.010 1104 -7300 -210.2573 0.010 1104 -7400 -210.2490 0.010 1104 -7500 -210.2258 0.010 1104 -7600 -210.2188 0.010 1104 -7700 -210.1885 0.010 1104 -7800 -210.1675 0.010 1104 -7900 -210.1664 0.010 1104 -8000 -210.1658 0.010 1104 -8100 -210.1138 0.010 1104 -8200 -210.1029 0.010 1104 -8300 -210.0913 0.010 1104 -8400 -210.0890 0.010 1104 -8500 -210.0862 0.010 1104 -8600 -210.0634 0.010 1104 -8700 -210.0288 0.010 1104 -8800 -210.0035 0.010 8716 -8900 -210.0028 0.010 8716 -9000 -209.9601 0.010 8716 -9100 -209.9395 0.010 8716 -9200 -209.9370 0.010 8716 -9300 -209.9252 0.010 8716 -9400 -209.9226 0.010 8716 -9500 -209.9207 0.010 8716 -9600 -209.9191 0.010 8716 -9700 -209.9035 0.010 8716 -9800 -209.8885 0.010 8716 -9900 -209.8794 0.010 8716 -10000 -209.8437 0.010 8716 - Optimizing parameters... improved 0.519 lnL - Optimizing branchlengths... improved 0.016 lnL -NOTE: ****Specified generation limit (10000) reached... +4205 -210.6724 0.010 1104 +4300 -210.6524 0.010 1104 +4400 -210.6492 0.010 1104 +4500 -210.6477 0.010 1104 +Reached termination condition! +last topological improvement at gen 1104 +Improvement over last 500 gen = 0.04689 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 5.724, AG = 9.823, AT = 0.264, CG = 10.186, CT = 15.625, GT = 1.000 + AC = 2.570, AG = 4.891, AT = 0.202, CG = 4.460, CT = 7.250, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2335 0.3288 0.2091 0.2286 + (ACGT) 0.2331 0.3366 0.2107 0.2196 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 4.4640 + 1.1902 with an invariant (invariable) site category, proportion estimated - 0.2923 + 0.1209 Substitution rate categories under this model: rate proportion - 0.0000 0.2923 - 0.5336 0.2359 - 0.9309 0.2359 - 1.5355 0.2359 + 0.0000 0.1209 + 0.2293 0.2930 + 0.7543 0.2930 + 2.0164 0.2930 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 1 branches were collapsed. Saving site likelihoods to file ch.n.G3.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 : -209.3089 +Replicate 1 : -210.6477 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: 5.724 9.823 0.2637 10.19 15.62 1 0.233 0.329 0.209 0.229 4.464 0.292 +rep 1: 2.57 4.891 0.2023 4.46 7.25 1 0.233 0.337 0.211 0.220 1.190 0.121 Treelengths: TL -rep 1: 2.261 +rep 1: 2.247 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf @@ -15993,27 +15964,6 @@ 2600 -166.3862 0.010 843 2800 -166.3657 0.010 843 3000 -166.3070 0.010 843 -3200 -166.2787 0.010 843 -3400 -166.2099 0.010 843 -3600 -166.0618 0.010 843 -3800 -165.9521 0.010 843 -4000 -165.9340 0.010 843 -4200 -165.8876 0.010 843 -4400 -165.8800 0.010 843 -4600 -165.7809 0.010 843 -4800 -165.7682 0.010 843 -5000 -165.6807 0.010 843 -5200 -165.6629 0.010 843 -5400 -165.5966 0.010 843 -5600 -165.4767 0.010 843 -5800 -165.3754 0.010 843 -6000 -165.2856 0.010 843 -6200 -165.2442 0.010 6021 -6400 -165.1354 0.010 6021 -6600 -165.0479 0.010 6021 -6800 -165.0428 0.010 6021 -7000 -164.8383 0.010 6021 -7200 -164.6664 0.010 6021 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16094,63 +16044,55 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 7358, seed 1864093106, best lnL -164.661 +Bootstrap rep 1 (of 1) generation 3000, seed 1077187659, best lnL -166.307 gen current_lnL precision last_tree_imp -7358 -164.6613 0.010 6021 -7400 -164.6478 0.010 6021 -7500 -164.6472 0.010 6021 -7600 -164.5352 0.010 7573 -7700 -164.4035 0.010 7573 -7800 -164.3902 0.010 7573 -7900 -164.3595 0.010 7573 -8000 -164.3323 0.010 7573 -8100 -164.1711 0.010 7573 -8200 -164.1537 0.010 7573 -8300 -164.0538 0.010 7573 -8400 -164.0465 0.010 7573 -8500 -164.0049 0.010 7573 -8600 -163.9411 0.010 7573 -8700 -163.8406 0.010 7573 -8800 -163.8133 0.010 7573 -8900 -163.8024 0.010 7573 -9000 -163.7249 0.010 7573 -9100 -163.7136 0.010 7573 -9200 -163.7035 0.010 7573 -9300 -163.6573 0.010 7573 -9400 -163.6398 0.010 7573 -9500 -163.5644 0.010 7573 -9600 -163.5152 0.010 7573 -9700 -163.4697 0.010 7573 -9800 -163.4652 0.010 7573 -9900 -163.4587 0.010 7573 -10000 -163.4575 0.010 7573 - Optimizing parameters... improved 1.431 lnL - Optimizing branchlengths... improved 0.011 lnL -NOTE: ****Specified generation limit (10000) reached... +3000 -166.3070 0.010 843 +3100 -166.2830 0.010 843 +3200 -166.2787 0.010 843 +3300 -166.2763 0.010 843 +3400 -166.2099 0.010 843 +3500 -166.0931 0.010 843 +3600 -166.0618 0.010 843 +3700 -166.0204 0.010 843 +3800 -165.9521 0.010 843 +3900 -165.9405 0.010 843 +4000 -165.9340 0.010 843 +4100 -165.9078 0.010 843 +4200 -165.8876 0.010 843 +4300 -165.8812 0.010 843 +4400 -165.8800 0.010 843 +4500 -165.8545 0.010 843 +4600 -165.7809 0.010 843 +4700 -165.7799 0.010 843 +4800 -165.7682 0.010 843 +4900 -165.6827 0.010 843 +5000 -165.6807 0.010 843 +NOTE: ****Specified time limit (5 seconds) reached... -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.785, AG = 10.721, AT = 2.714, CG = 4.252, CT = 44.709, GT = 1.000 + AC = 0.573, AG = 6.924, AT = 0.932, CG = 2.542, CT = 11.717, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1323 0.4184 0.2444 0.2049 + (ACGT) 0.1311 0.4050 0.2325 0.2314 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 38.8673 + 2.0604 with an invariant (invariable) site category, proportion estimated - 0.3493 + 0.2469 Substitution rate categories under this model: rate proportion - 0.0000 0.3493 - 0.8041 0.1627 - 0.9408 0.1627 - 1.0445 0.1627 - 1.2106 0.1627 + 0.0000 0.2469 + 0.3004 0.1883 + 0.6613 0.1883 + 1.0714 0.1883 + 1.9669 0.1883 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 2 branches were collapsed. +>>>Terminated Bootstrap rep 1 (of 1) <<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16160,15 +16102,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -162.0150 +Replicate 1 : -165.6634 (TERMINATED PREMATURELY) 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: 0.7854 10.72 2.714 4.252 44.71 1 0.132 0.418 0.244 0.205 38.867 0.349 +rep 1: 0.5727 6.924 0.9316 2.542 11.72 1 0.131 0.405 0.233 0.231 2.060 0.247 Treelengths: TL -rep 1: 3.333 +rep 1: 2.115 Saving best tree to bootstrap file ch.n.G4.boot.tre @@ -16298,75 +16240,15 @@ 4600 -212.8794 0.010 3769 4800 -212.8766 0.010 3769 5000 -212.8761 0.010 3769 -5200 -212.8556 0.010 3769 -5400 -212.8534 0.010 3769 -5600 -212.8186 0.010 3769 -5800 -212.7686 0.010 3769 -6000 -212.7264 0.010 3769 -6200 -212.7248 0.010 3769 -6400 -212.7245 0.010 3769 -6600 -212.7155 0.010 3769 -6800 -212.7057 0.010 3769 -7000 -212.7025 0.010 3769 -7200 -212.7020 0.010 3769 -7400 -212.6750 0.010 3769 -7600 -212.6702 0.010 3769 -7800 -212.6661 0.010 3769 -8000 -212.6646 0.010 3769 -8200 -212.6594 0.010 3769 -8400 -212.6591 0.010 3769 -8600 -212.6390 0.010 3769 -8800 -212.5865 0.010 3769 -9000 -212.5495 0.010 3769 -9200 -212.5341 0.010 3769 -9400 -212.5173 0.010 3769 -9600 -212.4987 0.010 3769 -9800 -212.4933 0.010 3769 -10000 -212.4848 0.010 3769 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (10000) reached... - -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT -Model 1 - Number of states = 4 (nucleotide data) - Nucleotide Relative Rate Matrix: 6 rates - AC = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 - Rate Heterogeneity Model: - no rate heterogeneity - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be 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 : -212.4848 - -Parameter estimates: - r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.254 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 - -Treelengths: - TL -rep 1: 1.718 - -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 +NOTE: ****Specified time limit (5 seconds) reached... -WARNING: Internal states inferred on tree from prematurely terminated search +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. -####################################################### Running GARLI Version 2.1. () ->Single processor version for 32-bit OS<- ############################################################## @@ -16437,22 +16319,38 @@ STARTING RUN Restarting from checkpoint... - generation 10001, seed 1459438551, best lnL -212.485 + generation 5070, seed 27068809, best lnL -212.872 gen current_lnL precision last_tree_imp -10001 -212.4848 0.010 3769 +5070 -212.8724 0.010 3769 +5100 -212.8649 0.010 3769 +5200 -212.8556 0.010 3769 +5300 -212.8534 0.010 3769 +5400 -212.8534 0.010 3769 +5500 -212.8216 0.010 3769 +5600 -212.8186 0.010 3769 +5700 -212.8106 0.010 3769 +5800 -212.7686 0.010 3769 +5900 -212.7273 0.010 3769 +6000 -212.7264 0.010 3769 +6100 -212.7249 0.010 3769 +6200 -212.7248 0.010 3769 +6300 -212.7245 0.010 3769 +Reached termination condition! +last topological improvement at gen 3769 +Improvement over last 500 gen = 0.04407 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 8.254, AG = 15.546, AT = 0.648, CG = 15.522, CT = 10.081, GT = 1.000 + AC = 4.838, AG = 9.614, AT = 0.397, CG = 9.745, CT = 6.242, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2186 0.2862 0.1832 0.3120 + (ACGT) 0.2212 0.2915 0.1818 0.3056 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... @@ -16460,15 +16358,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -212.4848 +Replicate 1 : -212.7245 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 8.254 15.55 0.6481 15.52 10.08 1 0.219 0.286 0.183 0.312 +rep 1: 4.838 9.614 0.397 9.745 6.242 1 0.221 0.291 0.182 0.306 Treelengths: TL -rep 1: 1.718 +rep 1: 1.732 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 @@ -16604,35 +16502,6 @@ 2200 -210.8961 0.010 1502 2400 -210.8906 0.010 1502 2600 -210.8173 0.010 1502 -2800 -210.7848 0.010 1502 -3000 -210.7511 0.010 2883 -3200 -210.7243 0.010 2883 -3400 -210.7006 0.010 2883 -3600 -210.6993 0.010 2883 -3800 -210.6779 0.010 2883 -4000 -210.6776 0.010 2883 -4200 -210.6505 0.010 2883 -4400 -210.6306 0.010 2883 -4600 -210.6208 0.010 2883 -4800 -210.5769 0.010 2883 -5000 -210.5647 0.010 2883 -5200 -210.5368 0.010 2883 -5400 -210.5093 0.010 2883 -5600 -210.4832 0.010 2883 -5800 -210.3736 0.010 2883 -6000 -210.3408 0.010 2883 -6200 -210.3319 0.010 2883 -6400 -210.3259 0.010 2883 -6600 -210.2891 0.010 2883 -6800 -210.2615 0.010 2883 -7000 -210.2579 0.010 2883 -7200 -210.2571 0.010 2883 -7400 -210.2287 0.010 2883 -7600 -210.2174 0.010 2883 -7800 -210.1382 0.010 7783 -8000 -210.1300 0.010 7783 -8200 -210.1282 0.010 7783 -8400 -210.1160 0.010 7783 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16720,49 +16589,71 @@ STARTING RUN Restarting from checkpoint... - generation 8472, seed 1640621176, best lnL -210.081 + generation 2781, seed 424468205, best lnL -210.791 gen current_lnL precision last_tree_imp -8472 -210.0809 0.010 7783 -8500 -210.0806 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 -209.9556 0.010 7783 -9100 -209.9410 0.010 7783 -9200 -209.9334 0.010 7783 -9300 -209.9309 0.010 7783 -9400 -209.9300 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 +2781 -210.7908 0.010 1502 +2800 -210.7848 0.010 1502 +2900 -210.7571 0.010 2883 +3000 -210.7511 0.010 2883 +3100 -210.7475 0.010 2883 +3200 -210.7243 0.010 2883 +3300 -210.7026 0.010 2883 +3400 -210.7006 0.010 2883 +3500 -210.7006 0.010 2883 +3600 -210.6993 0.010 2883 +3700 -210.6820 0.010 2883 +3800 -210.6779 0.010 2883 +3900 -210.6776 0.010 2883 +4000 -210.6776 0.010 2883 +4100 -210.6581 0.010 2883 +4200 -210.6505 0.010 2883 +4300 -210.6473 0.010 2883 +4400 -210.6306 0.010 2883 +4500 -210.6277 0.010 2883 +4600 -210.6208 0.010 2883 +4700 -210.5907 0.010 2883 +4800 -210.5769 0.010 2883 +4900 -210.5673 0.010 2883 +5000 -210.5647 0.010 2883 +5100 -210.5566 0.010 2883 +5200 -210.5368 0.010 2883 +5300 -210.5127 0.010 2883 +5400 -210.5093 0.010 2883 +5500 -210.5012 0.010 2883 +5600 -210.4832 0.010 2883 +5700 -210.4040 0.010 2883 +5800 -210.3736 0.010 2883 +5900 -210.3639 0.010 2883 +6000 -210.3408 0.010 2883 +6100 -210.3320 0.010 2883 +6200 -210.3319 0.010 2883 +6300 -210.3311 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 = 0.04248 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 = 4.762, CT = 8.462, GT = 1.000 + AC = 2.168, AG = 4.001, AT = 0.207, CG = 3.857, CT = 7.381, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2433 0.3351 0.2122 0.2095 + (ACGT) 0.2427 0.3358 0.2126 0.2089 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 2.2903 + 1.4302 with an invariant (invariable) site category, proportion estimated - 0.2309 + 0.1984 Substitution rate categories under this model: rate proportion - 0.0000 0.2309 - 0.3256 0.1923 - 0.6827 0.1923 - 1.0758 0.1923 - 1.9159 0.1923 + 0.0000 0.1984 + 0.2143 0.2004 + 0.5765 0.2004 + 1.0460 0.2004 + 2.1631 0.2004 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. NOTE: If collapsing of minimum length branches is requested (collapsebranches = 1) in a run with @@ -16775,15 +16666,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -209.8954 +Replicate 1 : -210.3311 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 4.762 8.462 1 0.243 0.335 0.212 0.210 2.290 0.231 +rep 1: 2.168 4.001 0.2071 3.857 7.381 1 0.243 0.336 0.213 0.209 1.430 0.198 Treelengths: TL -rep 1: 2.447 +rep 1: 2.397 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 @@ -16983,15 +16874,6 @@ 0 -13377.3893 0.500 0 100 -13375.8793 0.500 0 200 -13373.8435 0.500 0 -300 -13372.9677 0.500 0 -400 -13371.8985 0.500 0 -500 -13371.5864 0.500 0 -Optimization precision reduced - Optimizing parameters... improved 0.048 lnL - Optimizing branchlengths... improved 0.000 lnL -600 -13371.2064 0.402 0 -700 -13371.0754 0.402 0 -800 -13370.9489 0.402 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17114,15 +16996,10 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 826, seed 1057179346, best lnL -13370.893 +Bootstrap rep 1 (of 1) generation 235, seed 1698004276, best lnL -13373.673 gen current_lnL precision last_tree_imp -826 -13370.8929 0.402 0 -900 -13370.7802 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 +235 -13373.6733 0.500 0 +300 -13372.9677 0.500 0 NOTE: ****Specified time limit (1 seconds) reached... MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -17130,58 +17007,58 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.598, AG = 2.495, AT = 1.210, CG = 1.210, CT = 4.035, GT = 1.000 + AC = 1.292, AG = 2.180, AT = 1.069, CG = 1.069, CT = 3.293, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3110 0.1818 0.3061 0.2010 + (ACGT) 0.3109 0.1852 0.3040 0.1998 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3640 + 0.3450 Substitution rate categories under this model: rate proportion - 0.0119 0.2500 - 0.1544 0.2500 - 0.6892 0.2500 - 3.1446 0.2500 + 0.0096 0.2500 + 0.1396 0.2500 + 0.6641 0.2500 + 3.1866 0.2500 Model 2 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 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 + AC = 2.813, AG = 4.206, AT = 0.866, CG = 4.206, CT = 2.813, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2791 0.1777 0.1601 0.3830 + (ACGT) 0.2826 0.1738 0.1612 0.3824 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2460 + 0.2509 Substitution rate categories under this model: rate proportion - 0.0019 0.2500 - 0.0638 0.2500 - 0.4929 0.2500 - 3.4413 0.2500 + 0.0022 0.2500 + 0.0673 0.2500 + 0.5033 0.2500 + 3.4272 0.2500 Model 3 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 3 1 0 ) - AC = 1.000, AG = 5.347, AT = 4.290, CG = 0.632, CT = 5.347, GT = 1.000 + AC = 1.000, AG = 5.442, AT = 4.447, CG = 0.651, CT = 5.442, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1555 0.3460 0.2769 0.2216 + (ACGT) 0.1555 0.3445 0.2785 0.2215 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1101 + 3.7874 with an invariant (invariable) site category, proportion estimated - 0.0486 + 0.0448 Substitution rate categories under this model: rate proportion - 0.0000 0.0486 - 0.4603 0.2379 - 0.7789 0.2379 - 1.0844 0.2379 - 1.6764 0.2379 + 0.0000 0.0448 + 0.4423 0.2388 + 0.7675 0.2388 + 1.0844 0.2388 + 1.7058 0.2388 Subset rate multipliers: - 0.53 0.29 2.18 + 0.52 0.29 2.19 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be collapsed. @@ -17195,25 +17072,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.5606 (TERMINATED PREMATURELY) +Replicate 1 : -13372.3254 (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 4.035 1 0.311 0.182 0.306 0.201 0.364 +rep 1: 1.292 2.18 1.069 1.069 3.293 1 0.311 0.185 0.304 0.200 0.345 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: 2.813 4.206 0.8659 4.206 2.813 1 0.283 0.174 0.161 0.382 0.251 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 -rep 1: 1 5.347 4.29 0.6325 5.347 1 0.156 0.346 0.277 0.222 4.110 0.049 +rep 1: 1 5.442 4.447 0.6508 5.442 1 0.155 0.345 0.278 0.222 3.787 0.045 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.772 0.530 0.287 2.183 +rep 1: 1.765 0.521 0.286 2.193 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17384,147 +17261,6 @@ 300 -467.7641 0.010 76 400 -467.7601 0.010 76 500 -467.7562 0.010 76 -600 -467.7484 0.010 76 -700 -467.7453 0.010 76 -800 -467.7426 0.010 76 -900 -467.7420 0.010 76 -1000 -467.7408 0.010 76 -1100 -467.7395 0.010 76 -1200 -467.7384 0.010 76 -1300 -467.7383 0.010 76 -1400 -467.7371 0.010 76 -1500 -467.7350 0.010 76 -1600 -467.7322 0.010 76 -1700 -467.7288 0.010 76 -1800 -467.7270 0.010 76 -1900 -467.7270 0.010 76 -2000 -467.7247 0.010 76 -2100 -467.7240 0.010 76 -2200 -467.7237 0.010 76 -2300 -467.7235 0.010 76 -2400 -467.7217 0.010 76 -2500 -467.7212 0.010 76 -2600 -467.7209 0.010 76 -2700 -467.7204 0.010 76 -2800 -467.7202 0.010 76 -2900 -467.7200 0.010 76 -3000 -467.7200 0.010 76 -3100 -467.7184 0.010 76 -3200 -467.7183 0.010 76 -3300 -467.7165 0.010 76 -3400 -467.7165 0.010 76 -3500 -467.7162 0.010 76 -3600 -467.7160 0.010 76 -3700 -467.7160 0.010 76 -3800 -467.7159 0.010 76 -Reached termination condition! -last topological improvement at gen 76 -Improvement over last 500 gen = 0.00059 -Current score = -467.7159 -Performing final optimizations... -pass 1 : -467.7120 (branch= 0.0000 subset rates= 0.0039) -pass 2 : -467.6911 (branch= 0.0209 subset rates= 0.0000) -pass 3 : -467.6869 (branch= 0.0042 subset rates= 0.0000) -pass 4 : -467.6843 (branch= 0.0026 subset rates= 0.0000) -pass 5 : -467.6817 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -467.6803 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -467.6795 (branch= 0.0007 subset rates= 0.0001) -pass 8 : -467.6788 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6783 (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 4 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.48 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1831048457 - -Initial ln Likelihood: -637.1584 -optimizing: starting branch lengths, subset rates... -pass 1:+ 151.120 (branch= 144.13 scale= 2.32 subset rates= 4.67) -pass 2:+ 14.959 (branch= 13.95 scale= 0.00 subset rates= 1.01) -pass 3:+ 2.985 (branch= 2.78 scale= 0.01 subset rates= 0.19) -pass 4:+ 0.213 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.025 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8409 -gen current_lnL precision last_tree_imp -0 -467.8409 0.010 0 -100 -467.8006 0.010 88 -200 -467.7829 0.010 88 -300 -467.7645 0.010 88 -400 -467.7572 0.010 88 -500 -467.7508 0.010 88 -600 -467.7420 0.010 88 -700 -467.7377 0.010 88 -800 -467.7326 0.010 88 -900 -467.7300 0.010 88 -1000 -467.7251 0.010 88 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17650,274 +17386,52 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1036, seed 1879992365, best lnL -467.722 -gen current_lnL precision last_tree_imp -1036 -467.7221 0.010 88 -1100 -467.7186 0.010 88 -1200 -467.7174 0.010 88 -1300 -467.7143 0.010 88 -1400 -467.7139 0.010 88 -1500 -467.7130 0.010 88 -1600 -467.7128 0.010 88 -1700 -467.7101 0.010 88 -1800 -467.7076 0.010 88 -1900 -467.7072 0.010 88 -2000 -467.7065 0.010 88 -2100 -467.7061 0.010 88 -2200 -467.7057 0.010 88 -2300 -467.7052 0.010 88 -2400 -467.7043 0.010 88 -2500 -467.7039 0.010 88 -2600 -467.7039 0.010 88 -2700 -467.7038 0.010 88 -2800 -467.7036 0.010 88 -2900 -467.7035 0.010 88 -Reached termination condition! -last topological improvement at gen 88 -Improvement over last 500 gen = 0.00077 -Current score = -467.7035 -Performing final optimizations... -pass 1 : -467.7035 (branch= 0.0000 subset rates= 0.0001) -pass 2 : -467.6923 (branch= 0.0112 subset rates= 0.0000) -pass 3 : -467.6861 (branch= 0.0060 subset rates= 0.0001) -pass 4 : -467.6835 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -467.6821 (branch= 0.0013 subset rates= 0.0000) -pass 6 : -467.6810 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -467.6801 (branch= 0.0009 subset rates= 0.0000) -pass 8 : -467.6795 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6792 (branch= 0.0003 subset rates= 0.0000) -pass 10: -467.6789 (branch= 0.0002 subset rates= 0.0001) -pass 11: -467.6788 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6787 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6787 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6787 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6787 -Time used so far = 0 hours, 0 minutes and 8 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.47 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 2 (of 5)<<< - ->>>Search rep 3 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=387765568 - -Initial ln Likelihood: -629.3844 -optimizing: starting branch lengths, subset rates... -pass 1:+ 145.913 (branch= 138.38 scale= 3.36 subset rates= 4.18) -pass 2:+ 12.537 (branch= 11.64 scale= 0.00 subset rates= 0.90) -pass 3:+ 2.852 (branch= 2.62 scale= 0.06 subset rates= 0.18) -pass 4:+ 0.211 (branch= 0.21 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.034 (branch= 0.03 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8378 +Search rep 1 (of 5) generation 593, seed 303566572, best lnL -467.748 gen current_lnL precision last_tree_imp -0 -467.8378 0.010 0 -100 -467.8202 0.010 0 -200 -467.7910 0.010 0 -300 -467.7852 0.010 0 -400 -467.7649 0.010 0 -500 -467.7557 0.010 0 -600 -467.7482 0.010 0 -700 -467.7383 0.010 0 -800 -467.7308 0.010 0 -900 -467.7283 0.010 0 -1000 -467.7269 0.010 0 -1100 -467.7258 0.010 0 -1200 -467.7235 0.010 0 -1300 -467.7213 0.010 0 -1400 -467.7173 0.010 0 -1500 -467.7162 0.010 0 -1600 -467.7145 0.010 0 -1700 -467.7136 0.010 0 -1800 -467.7115 0.010 0 -1900 -467.7100 0.010 0 -2000 -467.7098 0.010 0 -2100 -467.7097 0.010 0 -2200 -467.7095 0.010 0 -2300 -467.7095 0.010 0 -2400 -467.7094 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00061 -Current score = -467.7094 -Performing final optimizations... -pass 1 : -467.7094 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6977 (branch= 0.0116 subset rates= 0.0001) -pass 3 : -467.6920 (branch= 0.0057 subset rates= 0.0000) -pass 4 : -467.6870 (branch= 0.0050 subset rates= 0.0000) -pass 5 : -467.6847 (branch= 0.0023 subset rates= 0.0000) -pass 6 : -467.6819 (branch= 0.0028 subset rates= 0.0000) -pass 7 : -467.6797 (branch= 0.0019 subset rates= 0.0003) -pass 8 : -467.6790 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -467.6786 (branch= 0.0004 subset rates= 0.0000) -pass 10: -467.6784 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 15: -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 - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.79 1.48 2.18 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 3 (of 5)<<< - ->>>Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=1057295975 - -Initial ln Likelihood: -639.3053 -optimizing: starting branch lengths, subset rates... -pass 1:+ 155.030 (branch= 149.66 scale= 1.11 subset rates= 4.26) -pass 2:+ 12.230 (branch= 11.21 scale= 0.06 subset rates= 0.97) -pass 3:+ 3.972 (branch= 3.84 scale= 0.00 subset rates= 0.13) -pass 4:+ 0.200 (branch= 0.18 scale= 0.02 subset rates= 0.00) -pass 5:+ 0.069 (branch= 0.05 scale= 0.01 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8049 -gen current_lnL precision last_tree_imp -0 -467.8049 0.010 0 -100 -467.7812 0.010 0 -200 -467.7731 0.010 0 -300 -467.7685 0.010 0 -400 -467.7534 0.010 301 -500 -467.7494 0.010 301 -600 -467.7430 0.010 301 +593 -467.7485 0.010 76 +600 -467.7484 0.010 76 +700 -467.7453 0.010 76 +800 -467.7426 0.010 76 +900 -467.7420 0.010 76 +1000 -467.7408 0.010 76 +1100 -467.7395 0.010 76 +1200 -467.7384 0.010 76 +1300 -467.7383 0.010 76 +1400 -467.7371 0.010 76 +1500 -467.7350 0.010 76 +1600 -467.7322 0.010 76 +1700 -467.7288 0.010 76 +1800 -467.7270 0.010 76 +1900 -467.7270 0.010 76 +2000 -467.7247 0.010 76 +2100 -467.7240 0.010 76 +2200 -467.7237 0.010 76 +2300 -467.7235 0.010 76 +2400 -467.7217 0.010 76 +2500 -467.7212 0.010 76 +2600 -467.7209 0.010 76 +2700 -467.7204 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7412 +Current score = -467.7204 Performing final optimizations... -pass 1 : -467.7400 (branch= 0.0000 subset rates= 0.0012) -pass 2 : -467.7111 (branch= 0.0288 subset rates= 0.0000) -pass 3 : -467.6988 (branch= 0.0124 subset rates= 0.0000) -pass 4 : -467.6906 (branch= 0.0082 subset rates= 0.0000) -pass 5 : -467.6872 (branch= 0.0034 subset rates= 0.0000) -pass 6 : -467.6828 (branch= 0.0031 subset rates= 0.0013) -pass 7 : -467.6807 (branch= 0.0020 subset rates= 0.0000) -pass 8 : -467.6801 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6793 (branch= 0.0003 subset rates= 0.0005) -pass 10: -467.6791 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6790 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6789 (branch= 0.0001 subset rates= 0.0000) -pass 13: -467.6789 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6789 (branch= 0.0000 subset rates= 0.0000) -pass 15: -467.6789 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7155 (branch= 0.0000 subset rates= 0.0049) +pass 2 : -467.6955 (branch= 0.0188 subset rates= 0.0011) +pass 3 : -467.6901 (branch= 0.0055 subset rates= 0.0000) +pass 4 : -467.6854 (branch= 0.0040 subset rates= 0.0007) +pass 5 : -467.6834 (branch= 0.0020 subset rates= 0.0000) +pass 6 : -467.6810 (branch= 0.0024 subset rates= 0.0000) +pass 7 : -467.6803 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -467.6796 (branch= 0.0008 subset rates= 0.0000) +pass 9 : -467.6794 (branch= 0.0002 subset rates= 0.0000) +pass 10: -467.6792 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6791 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0004) +pass 13: -467.6785 (branch= 0.0001 subset rates= 0.0000) +pass 14: -467.6785 (branch= 0.0000 subset rates= 0.0000) +pass 15: -467.6785 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -467.6789 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -467.6785 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -17945,11 +17459,11 @@ no rate heterogeneity Subset rate multipliers: - 0.79 1.48 2.16 + 0.79 1.48 2.17 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 1 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -17957,15 +17471,9 @@ ####################################################### -Completed 4 replicate search(es) (of 5). - -NOTE: Unless the following output indicates that search replicates found the - same topology, you should assume that they found different topologies. +Completed 1 replicate search(es) (of 5). Results: -Replicate 1 : -467.6782 -Replicate 2 : -467.6787 (same topology as 1) -Replicate 3 : -467.6782 (best) (same topology as 1) -Replicate 4 : -467.6789 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -467.6785 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17980,12 +17488,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.844 0.786 1.480 2.180 -rep 2: 3.839 0.788 1.472 2.178 -rep 3: 3.844 0.786 1.480 2.181 -rep 4: 3.841 0.787 1.482 2.162 +rep 1: 3.841 0.787 1.478 2.170 -Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -18156,145 +17661,6 @@ 600 -477.5298 0.010 373 700 -477.5290 0.010 373 800 -477.5213 0.010 373 -900 -477.5166 0.010 373 -1000 -477.5163 0.010 373 -1100 -477.5124 0.010 373 -1200 -477.5109 0.010 373 -1300 -477.5098 0.010 373 -1400 -477.4981 0.010 373 -1500 -477.4922 0.010 373 -1600 -477.4850 0.010 373 -1700 -477.4817 0.010 373 -1800 -477.4773 0.010 373 -1900 -477.4761 0.010 373 -2000 -477.4748 0.010 373 -2100 -477.4739 0.010 373 -2200 -477.4732 0.010 373 -2300 -477.4729 0.010 373 -2400 -477.4726 0.010 373 -2500 -477.4723 0.010 373 -2600 -477.4711 0.010 373 -2700 -477.4707 0.010 373 -2800 -477.4706 0.010 373 -2900 -477.4705 0.010 373 -3000 -477.4702 0.010 373 -3100 -477.4701 0.010 373 -Reached termination condition! -last topological improvement at gen 373 -Improvement over last 500 gen = 0.00099 -Current score = -477.4701 -Performing final optimizations... -pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0002) -pass 3 : -477.4394 (branch= 0.0036 subset rates= 0.0000) -pass 4 : -477.4366 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -477.4354 (branch= 0.0013 subset rates= 0.0000) -pass 6 : -477.4347 (branch= 0.0007 subset rates= 0.0000) -pass 7 : -477.4334 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -477.4324 (branch= 0.0010 subset rates= 0.0000) -pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0001) -pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -477.4316 -Time used so far = 0 hours, 0 minutes and 3 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.63 1.92 2.74 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mk model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=200420059 - -Initial ln Likelihood: -656.4902 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) -pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) -pass 3:+ 3.562 (branch= 2.11 scale= 0.00 subset rates= 1.45) -pass 4:+ 2.460 (branch= 2.02 scale= 0.00 subset rates= 0.44) -pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.745 (branch= 0.71 scale= 0.01 subset rates= 0.02) -pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8527 -gen current_lnL precision last_tree_imp -0 -477.8527 0.010 0 -100 -477.7879 0.010 74 -200 -477.7665 0.010 74 -300 -477.7486 0.010 74 -400 -477.7424 0.010 74 -500 -477.7295 0.010 74 -600 -477.7267 0.010 74 -700 -477.7205 0.010 74 -800 -477.7194 0.010 74 -900 -477.7186 0.010 74 -1000 -477.7135 0.010 74 -1100 -477.7094 0.010 74 -1200 -477.7090 0.010 74 -1300 -477.7060 0.010 74 -1400 -477.7036 0.010 74 -1500 -477.7019 0.010 74 -1600 -477.7004 0.010 74 -1700 -477.6994 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18420,56 +17786,54 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 1766, seed 274794359, best lnL -477.699 +Search rep 1 (of 5) generation 800, seed 354217079, best lnL -477.521 gen current_lnL precision last_tree_imp -1766 -477.6991 0.010 74 -1800 -477.6984 0.010 74 -1900 -477.6977 0.010 74 -2000 -477.6953 0.010 74 -2100 -477.3774 0.010 2081 -2200 -477.3631 0.010 2170 -2300 -477.3559 0.010 2170 -2400 -477.3497 0.010 2170 -2500 -477.3452 0.010 2170 -2600 -477.3293 0.010 2170 -2700 -477.3261 0.010 2170 -2800 -477.3186 0.010 2170 -2900 -477.3149 0.010 2170 -3000 -477.3144 0.010 2170 -3100 -477.3140 0.010 2170 -3200 -477.3125 0.010 2170 -3300 -477.3125 0.010 2170 -3400 -477.3123 0.010 2170 -3500 -477.3110 0.010 2170 -3600 -477.3109 0.010 2170 -3700 -477.3101 0.010 2170 -3800 -477.3085 0.010 2170 -3900 -477.3085 0.010 2170 -4000 -477.3085 0.010 2170 -4100 -477.3082 0.010 2170 -4200 -477.3082 0.010 2170 -4300 -477.3079 0.010 2170 +800 -477.5213 0.010 373 +900 -477.5166 0.010 373 +1000 -477.5163 0.010 373 +1100 -477.5124 0.010 373 +1200 -477.5109 0.010 373 +1300 -477.5098 0.010 373 +1400 -477.4981 0.010 373 +1500 -477.4922 0.010 373 +1600 -477.4850 0.010 373 +1700 -477.4817 0.010 373 +1800 -477.4773 0.010 373 +1900 -477.4761 0.010 373 +2000 -477.4748 0.010 373 +2100 -477.4739 0.010 373 +2200 -477.4732 0.010 373 +2300 -477.4729 0.010 373 +2400 -477.4726 0.010 373 +2500 -477.4723 0.010 373 +2600 -477.4711 0.010 373 +2700 -477.4707 0.010 373 +2800 -477.4706 0.010 373 +2900 -477.4705 0.010 373 +3000 -477.4702 0.010 373 +3100 -477.4701 0.010 373 Reached termination condition! -last topological improvement at gen 2170 -Improvement over last 500 gen = 0.00067 -Current score = -477.3079 +last topological improvement at gen 373 +Improvement over last 500 gen = 0.00099 +Current score = -477.4701 Performing final optimizations... -pass 1 : -477.2447 (branch= 0.0000 subset rates= 0.0632) -pass 2 : -477.2336 (branch= 0.0111 subset rates= 0.0000) -pass 3 : -477.2150 (branch= 0.0106 subset rates= 0.0080) -pass 4 : -477.2129 (branch= 0.0020 subset rates= 0.0000) -pass 5 : -477.2082 (branch= 0.0047 subset rates= 0.0000) -pass 6 : -477.2060 (branch= 0.0019 subset rates= 0.0003) -pass 7 : -477.2056 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -477.2049 (branch= 0.0006 subset rates= 0.0001) -pass 9 : -477.2047 (branch= 0.0002 subset rates= 0.0000) -pass 10: -477.2046 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2045 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.2045 (branch= 0.0000 subset rates= 0.0000) -pass 13: -477.2045 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.4701 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4430 (branch= 0.0269 subset rates= 0.0002) +pass 3 : -477.4394 (branch= 0.0036 subset rates= 0.0000) +pass 4 : -477.4366 (branch= 0.0027 subset rates= 0.0000) +pass 5 : -477.4354 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -477.4347 (branch= 0.0007 subset rates= 0.0000) +pass 7 : -477.4334 (branch= 0.0013 subset rates= 0.0000) +pass 8 : -477.4324 (branch= 0.0010 subset rates= 0.0000) +pass 9 : -477.4321 (branch= 0.0004 subset rates= 0.0000) +pass 10: -477.4319 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.4316 (branch= 0.0001 subset rates= 0.0001) +pass 13: -477.4316 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4316 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.2045 -Time used so far = 0 hours, 0 minutes and 9 seconds +Final score = -477.4316 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18497,13 +17861,13 @@ no rate heterogeneity Subset rate multipliers: - 0.64 1.93 2.63 + 0.63 1.92 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Completed Search rep 2 (of 5)<<< +>>>Completed Search rep 1 (of 5)<<< ->>>Search rep 3 (of 5)<<< +>>>Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) Model 1 @@ -18532,64 +17896,61 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=1602142636 +Starting with seed=200420059 -Initial ln Likelihood: -662.4976 +Initial ln Likelihood: -656.4902 optimizing: starting branch lengths, subset rates... -pass 1:+ 159.344 (branch= 147.93 scale= 1.33 subset rates= 10.09) -pass 2:+ 18.362 (branch= 14.32 scale= 0.01 subset rates= 4.02) -pass 3:+ 5.723 (branch= 4.51 scale= 0.00 subset rates= 1.22) -pass 4:+ 1.012 (branch= 0.74 scale= 0.00 subset rates= 0.28) -pass 5:+ 0.186 (branch= 0.17 scale= 0.00 subset rates= 0.02) -pass 6:+ 0.016 (branch= 0.00 scale= 0.02 subset rates= 0.00) -pass 7:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 1:+ 148.906 (branch= 137.62 scale= 1.92 subset rates= 9.37) +pass 2:+ 19.722 (branch= 15.83 scale= 0.00 subset rates= 3.89) +pass 3:+ 3.562 (branch= 2.11 scale= 0.00 subset rates= 1.45) +pass 4:+ 2.460 (branch= 2.02 scale= 0.00 subset rates= 0.44) +pass 5:+ 3.227 (branch= 3.23 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.745 (branch= 0.71 scale= 0.01 subset rates= 0.02) +pass 7:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 8:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8200 +lnL after optimization: -477.8527 gen current_lnL precision last_tree_imp -0 -477.8200 0.010 0 -100 -477.7127 0.010 12 -200 -477.6994 0.010 12 -300 -477.6923 0.010 12 -400 -477.5173 0.010 372 -500 -477.5116 0.010 372 -600 -477.5057 0.010 372 -700 -477.4981 0.010 372 -800 -477.4917 0.010 372 -900 -477.4851 0.010 372 -1000 -477.4827 0.010 372 -1100 -477.4798 0.010 372 -1200 -477.4747 0.010 372 -1300 -477.4729 0.010 372 -1400 -477.4704 0.010 372 -1500 -477.4686 0.010 372 -1600 -477.4673 0.010 372 -1700 -477.4649 0.010 372 -1800 -477.4647 0.010 372 -1900 -477.4633 0.010 372 -2000 -477.4630 0.010 372 -2100 -477.4621 0.010 372 -2200 -477.4620 0.010 372 +0 -477.8527 0.010 0 +100 -477.7879 0.010 74 +200 -477.7665 0.010 74 +300 -477.7486 0.010 74 +400 -477.7424 0.010 74 +500 -477.7295 0.010 74 +600 -477.7267 0.010 74 +700 -477.7205 0.010 74 +800 -477.7194 0.010 74 +900 -477.7186 0.010 74 +1000 -477.7135 0.010 74 +1100 -477.7094 0.010 74 +1200 -477.7090 0.010 74 +1300 -477.7060 0.010 74 +1400 -477.7036 0.010 74 +1500 -477.7019 0.010 74 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4604 +Current score = -477.7010 Performing final optimizations... -pass 1 : -477.4592 (branch= 0.0000 subset rates= 0.0013) -pass 2 : -477.4450 (branch= 0.0142 subset rates= 0.0000) -pass 3 : -477.4386 (branch= 0.0064 subset rates= 0.0000) -pass 4 : -477.4380 (branch= 0.0006 subset rates= 0.0000) -pass 5 : -477.4358 (branch= 0.0022 subset rates= 0.0000) -pass 6 : -477.4342 (branch= 0.0016 subset rates= 0.0000) -pass 7 : -477.4328 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -477.4323 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -477.4318 (branch= 0.0003 subset rates= 0.0001) -pass 10: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.4316 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4316 (branch= 0.0000 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 1 : -477.6833 (branch= 0.0116 subset rates= 0.0060) +pass 2 : -477.6533 (branch= 0.0236 subset rates= 0.0064) +pass 3 : -477.6425 (branch= 0.0108 subset rates= 0.0000) +pass 4 : -477.6354 (branch= 0.0071 subset rates= 0.0000) +pass 5 : -477.6279 (branch= 0.0042 subset rates= 0.0033) +pass 6 : -477.6227 (branch= 0.0031 subset rates= 0.0021) +pass 7 : -477.6202 (branch= 0.0025 subset rates= 0.0000) +pass 8 : -477.6189 (branch= 0.0013 subset rates= 0.0000) +pass 9 : -477.6182 (branch= 0.0007 subset rates= 0.0000) +pass 10: -477.6177 (branch= 0.0005 subset rates= 0.0000) +pass 11: -477.6174 (branch= 0.0002 subset rates= 0.0000) +pass 12: -477.6173 (branch= 0.0001 subset rates= 0.0001) +pass 13: -477.6170 (branch= 0.0001 subset rates= 0.0002) +pass 14: -477.6169 (branch= 0.0001 subset rates= 0.0000) +pass 15: -477.6168 (branch= 0.0001 subset rates= 0.0000) +pass 16: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 17: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 18: -477.6168 (branch= 0.0000 subset rates= 0.0000) +pass 19: -477.6168 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4315 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -477.6167 +Time used so far = 0 hours, 0 minutes and 16 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -18619,9 +17980,9 @@ Subset rate multipliers: 0.63 1.91 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 branches were collapsed. ->>>Terminated Search rep 3 (of 5)<<< +>>>Terminated Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -18629,14 +17990,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: -Replicate 1 : -477.4316 -Replicate 2 : -477.2045 (best) -Replicate 3 : -477.4315 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -477.4316 (best) +Replicate 2 : -477.6167 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18652,10 +18012,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.930 0.631 1.917 2.740 -rep 2: 4.695 0.635 1.931 2.634 -rep 3: 4.928 0.632 1.914 2.739 +rep 2: 4.894 0.633 1.911 2.739 -Saving final tree from best search rep (#2) to ch.p.mkO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkv.ssr.conf @@ -18825,119 +18184,6 @@ 200 -427.7092 0.010 179 300 -426.9758 0.010 293 400 -425.6931 0.010 365 -500 -425.6675 0.010 365 -600 -425.6508 0.010 365 -700 -425.6316 0.010 365 -800 -425.6209 0.010 365 -900 -425.6123 0.010 365 -1000 -425.6089 0.010 365 -1100 -425.6081 0.010 365 -1200 -425.6057 0.010 365 -1300 -425.6039 0.010 365 -1400 -425.6034 0.010 365 -1500 -425.6029 0.010 365 -1600 -425.6020 0.010 365 -1700 -425.6018 0.010 365 -1800 -425.6014 0.010 365 -1900 -425.6001 0.010 365 -2000 -425.5991 0.010 365 -2100 -425.5979 0.010 365 -2200 -425.5930 0.010 365 -2300 -425.5915 0.010 365 -2400 -425.5913 0.010 365 -2500 -425.5897 0.010 365 -2600 -425.5895 0.010 365 -2700 -425.5894 0.010 365 -2800 -425.5890 0.010 365 -2900 -425.5876 0.010 365 -3000 -425.5875 0.010 365 -3100 -425.5854 0.010 365 -3200 -425.5852 0.010 365 -3300 -425.5851 0.010 365 -3400 -425.5828 0.010 365 -3500 -425.5828 0.010 365 -3600 -425.5827 0.010 365 -3700 -425.5827 0.010 365 -3800 -425.5826 0.010 365 -3900 -425.5824 0.010 365 -Reached termination condition! -last topological improvement at gen 365 -Improvement over last 500 gen = 0.00046 -Current score = -425.5824 -Performing final optimizations... -pass 1 : -425.5752 (branch= 0.0000 subset rates= 0.0071) -pass 2 : -425.5571 (branch= 0.0147 subset rates= 0.0034) -pass 3 : -425.5512 (branch= 0.0059 subset rates= 0.0000) -pass 4 : -425.5505 (branch= 0.0007 subset rates= 0.0000) -pass 5 : -425.5501 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -425.5497 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) -pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -425.5486 -Time used so far = 0 hours, 0 minutes and 4 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (standard data) - Character change matrix: - One rate (symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.87 1.53 1.12 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=255600397 - -Initial ln Likelihood: -577.2924 -optimizing: starting branch lengths, subset rates... -pass 1:+ 121.000 (branch= 120.23 scale= 0.75 subset rates= 0.02) -pass 2:+ 14.984 (branch= 14.74 scale= 0.04 subset rates= 0.20) -pass 3:+ 1.951 (branch= 1.90 scale= 0.00 subset rates= 0.05) -pass 4:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) -pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.3118 -gen current_lnL precision last_tree_imp -0 -439.3118 0.010 0 -100 -428.8361 0.010 97 -200 -428.0348 0.010 163 -300 -425.9017 0.010 248 -400 -425.7902 0.010 327 -500 -425.7309 0.010 411 -600 -425.6571 0.010 523 -700 -425.6380 0.010 523 -800 -425.6343 0.010 523 -900 -425.6312 0.010 523 -1000 -425.6253 0.010 523 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19066,58 +18312,65 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 1074, seed 1502474049, best lnL -425.624 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 400, seed 1135347809, best lnL -425.693 gen current_lnL precision last_tree_imp -1074 -425.6237 0.010 523 -1100 -425.6236 0.010 523 -1200 -425.6180 0.010 523 -1300 -425.6157 0.010 523 -1400 -425.6057 0.010 523 -1500 -425.6031 0.010 523 -1600 -425.5999 0.010 523 -1700 -425.5980 0.010 523 -1800 -425.5977 0.010 523 -1900 -425.5940 0.010 523 -2000 -425.5929 0.010 523 -2100 -425.5928 0.010 523 -2200 -425.5912 0.010 523 -2300 -425.5897 0.010 523 -2400 -425.5887 0.010 523 -2500 -425.5882 0.010 523 -2600 -425.5881 0.010 523 -2700 -425.5867 0.010 523 -2800 -425.5863 0.010 523 -2900 -425.5863 0.010 523 -3000 -425.5854 0.010 523 -3100 -425.5849 0.010 523 -3200 -425.5846 0.010 523 -3300 -425.5838 0.010 523 -3400 -425.5835 0.010 523 -3500 -425.5835 0.010 523 -3600 -425.5834 0.010 523 -3700 -425.5834 0.010 523 -3800 -425.5830 0.010 523 +400 -425.6931 0.010 365 +500 -425.6675 0.010 365 +600 -425.6508 0.010 365 +700 -425.6316 0.010 365 +800 -425.6209 0.010 365 +900 -425.6123 0.010 365 +1000 -425.6089 0.010 365 +1100 -425.6081 0.010 365 +1200 -425.6057 0.010 365 +1300 -425.6039 0.010 365 +1400 -425.6034 0.010 365 +1500 -425.6029 0.010 365 +1600 -425.6020 0.010 365 +1700 -425.6018 0.010 365 +1800 -425.6014 0.010 365 +1900 -425.6001 0.010 365 +2000 -425.5991 0.010 365 +2100 -425.5979 0.010 365 +2200 -425.5930 0.010 365 +2300 -425.5915 0.010 365 +2400 -425.5913 0.010 365 +2500 -425.5897 0.010 365 +2600 -425.5895 0.010 365 +2700 -425.5894 0.010 365 +2800 -425.5890 0.010 365 +2900 -425.5876 0.010 365 +3000 -425.5875 0.010 365 +3100 -425.5854 0.010 365 +3200 -425.5852 0.010 365 +3300 -425.5851 0.010 365 +3400 -425.5828 0.010 365 +3500 -425.5828 0.010 365 +3600 -425.5827 0.010 365 +3700 -425.5827 0.010 365 +3800 -425.5826 0.010 365 +3900 -425.5824 0.010 365 Reached termination condition! -last topological improvement at gen 523 -Improvement over last 500 gen = 0.00079 -Current score = -425.5830 +last topological improvement at gen 365 +Improvement over last 500 gen = 0.00046 +Current score = -425.5824 Performing final optimizations... -pass 1 : -425.5767 (branch= 0.0000 subset rates= 0.0062) -pass 2 : -425.5554 (branch= 0.0187 subset rates= 0.0026) -pass 3 : -425.5554 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -425.5514 (branch= 0.0021 subset rates= 0.0019) -pass 5 : -425.5509 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -425.5500 (branch= 0.0009 subset rates= 0.0000) -pass 7 : -425.5494 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -425.5492 (branch= 0.0002 subset rates= 0.0000) -pass 9 : -425.5489 (branch= 0.0000 subset rates= 0.0003) -pass 10: -425.5488 (branch= 0.0001 subset rates= 0.0000) +pass 1 : -425.5752 (branch= 0.0000 subset rates= 0.0071) +pass 2 : -425.5571 (branch= 0.0147 subset rates= 0.0034) +pass 3 : -425.5512 (branch= 0.0059 subset rates= 0.0000) +pass 4 : -425.5505 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -425.5501 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -425.5497 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -425.5493 (branch= 0.0004 subset rates= 0.0000) +pass 8 : -425.5490 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0003 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) pass 11: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.5487 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.5487 -Time used so far = 0 hours, 0 minutes and 9 seconds +Final score = -425.5486 +Time used so far = 0 hours, 0 minutes and 19 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19149,64 +18402,46 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 9 branches were collapsed. ->>>Completed Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< ->>>Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< Obtained starting tree 1 from Nexus -Starting with seed=124386023 +Starting with seed=255600397 -Initial ln Likelihood: -667.8582 +Initial ln Likelihood: -577.2924 optimizing: starting branch lengths, subset rates... -pass 1:+ 210.703 (branch= 209.92 scale= 0.77 subset rates= 0.01) -pass 2:+ 14.697 (branch= 14.50 scale= 0.07 subset rates= 0.12) -pass 3:+ 2.972 (branch= 2.91 scale= 0.03 subset rates= 0.04) -pass 4:+ 0.250 (branch= 0.24 scale= 0.01 subset rates= 0.00) -pass 5:+ 0.035 (branch= 0.04 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2013 +pass 1:+ 121.000 (branch= 120.23 scale= 0.75 subset rates= 0.02) +pass 2:+ 14.984 (branch= 14.74 scale= 0.04 subset rates= 0.20) +pass 3:+ 1.951 (branch= 1.90 scale= 0.00 subset rates= 0.05) +pass 4:+ 0.046 (branch= 0.05 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -439.3118 gen current_lnL precision last_tree_imp -0 -439.2013 0.010 0 -100 -429.9526 0.010 95 -200 -428.0661 0.010 184 -300 -425.6075 0.010 283 -400 -425.4842 0.010 312 -500 -425.4465 0.010 472 -600 -425.4348 0.010 472 -700 -425.4277 0.010 472 -800 -425.4227 0.010 472 -900 -425.3896 0.010 849 -1000 -425.3856 0.010 849 -1100 -425.3791 0.010 849 -1200 -425.3761 0.010 849 -1300 -425.3720 0.010 849 -1400 -425.3676 0.010 849 -1500 -425.3654 0.010 849 -1600 -425.3642 0.010 849 -1700 -425.3631 0.010 849 -1800 -425.3618 0.010 849 -1900 -425.3617 0.010 849 -2000 -425.3612 0.010 849 -2100 -425.3611 0.010 849 -2200 -425.3609 0.010 849 +0 -439.3118 0.010 0 +100 -428.8361 0.010 97 +200 -428.0348 0.010 163 +300 -425.9017 0.010 248 +400 -425.7902 0.010 327 +500 -425.7309 0.010 411 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.3609 +Current score = -425.6614 Performing final optimizations... -pass 1 : -425.3552 (branch= 0.0000 subset rates= 0.0057) -pass 2 : -425.3301 (branch= 0.0251 subset rates= 0.0000) -pass 3 : -425.3260 (branch= 0.0041 subset rates= 0.0000) -pass 4 : -425.3243 (branch= 0.0017 subset rates= 0.0000) -pass 5 : -425.3238 (branch= 0.0005 subset rates= 0.0000) -pass 6 : -425.3219 (branch= 0.0019 subset rates= 0.0000) -pass 7 : -425.3212 (branch= 0.0007 subset rates= 0.0000) -pass 8 : -425.3207 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -425.3205 (branch= 0.0002 subset rates= 0.0000) -pass 10: -425.3205 (branch= 0.0000 subset rates= 0.0000) -pass 11: -425.3204 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3204 (branch= 0.0000 subset rates= 0.0000) -pass 13: -425.3204 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.6339 (branch= 0.0186 subset rates= 0.0089) +pass 2 : -425.5802 (branch= 0.0514 subset rates= 0.0023) +pass 3 : -425.5630 (branch= 0.0172 subset rates= 0.0000) +pass 4 : -425.5537 (branch= 0.0093 subset rates= 0.0000) +pass 5 : -425.5510 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -425.5497 (branch= 0.0013 subset rates= 0.0000) +pass 7 : -425.5490 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -425.5489 (branch= 0.0001 subset rates= 0.0000) +pass 9 : -425.5487 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.5487 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.5486 (branch= 0.0000 subset rates= 0.0000) +pass 13: -425.5486 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -425.3204 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -425.5486 +Time used so far = 0 hours, 0 minutes and 20 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -19234,11 +18469,11 @@ no rate heterogeneity Subset rate multipliers: - 0.86 1.54 1.15 + 0.87 1.53 1.12 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 10 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -19246,14 +18481,13 @@ ####################################################### -Completed 3 replicate search(es) (of 5). +Completed 2 replicate search(es) (of 5). NOTE: Unless the following output indicates that search replicates found the same topology, you should assume that they found different topologies. Results: Replicate 1 : -425.5486 -Replicate 2 : -425.5487 (same topology as 1) -Replicate 3 : -425.3204 (best) (TERMINATED PREMATURELY) +Replicate 2 : -425.5486 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19269,10 +18503,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 3.037 0.868 1.530 1.116 -rep 2: 3.039 0.869 1.526 1.120 -rep 3: 2.980 0.865 1.539 1.149 +rep 2: 3.037 0.868 1.531 1.122 -Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#2) to bootstrap file ch.p.mkv.ssr.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### @@ -19442,139 +18675,6 @@ 200 -474.7186 0.010 68 300 -474.6982 0.010 68 400 -474.6395 0.010 329 -500 -474.1549 0.010 455 -600 -474.1345 0.010 560 -700 -474.0337 0.010 653 -800 -474.0224 0.010 653 -900 -474.0129 0.010 653 -1000 -474.0072 0.010 653 -1100 -474.0048 0.010 653 -1200 -474.0017 0.010 653 -1300 -473.9998 0.010 653 -1400 -473.9960 0.010 653 -1500 -473.9930 0.010 653 -1600 -473.9888 0.010 653 -1700 -473.9875 0.010 653 -1800 -473.9857 0.010 653 -1900 -473.9846 0.010 653 -2000 -473.9839 0.010 653 -2100 -473.9834 0.010 653 -2200 -473.9820 0.010 653 -2300 -473.9814 0.010 653 -2400 -473.9804 0.010 653 -2500 -473.9804 0.010 653 -2600 -473.9801 0.010 653 -2700 -473.9793 0.010 653 -2800 -473.9779 0.010 653 -2900 -473.9777 0.010 653 -3000 -473.9777 0.010 653 -3100 -473.9773 0.010 653 -3200 -473.9772 0.010 653 -3300 -473.9770 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00088 -Current score = -473.9770 -Performing final optimizations... -pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) -pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) -pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) -pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) -pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) -pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) -pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9507 -Time used so far = 0 hours, 0 minutes and 4 seconds - -MODEL REPORT - Parameter values are FINAL -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 0.59 2.07 2.80 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. - ->>>Completed Search rep 1 (of 5)<<< - ->>>Search rep 2 (of 5)<<< -Obtained starting tree 1 from Nexus -MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) -Model 1 - Number of states = 2 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.50, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 2 - Number of states = 3 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.33, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Model 3 - Number of states = 4 (ordered standard data) - Character change matrix: - One rate (ordered symmetric one rate Mkv model) - Equilibrium State Frequencies: equal (0.25, fixed) - Rate Heterogeneity Model: - no rate heterogeneity - -Subset rate multipliers: - 1.00 1.00 1.00 -Starting with seed=2125680066 - -Initial ln Likelihood: -649.8224 -optimizing: starting branch lengths, subset rates... -pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) -pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) -pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) -pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) -pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) -pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8071 -gen current_lnL precision last_tree_imp -0 -474.8071 0.010 0 -100 -474.7912 0.010 0 -200 -474.7021 0.010 123 -300 -474.5642 0.010 272 -400 -474.5190 0.010 272 -500 -474.5075 0.010 272 -600 -474.5034 0.010 272 -700 -474.4997 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19700,75 +18800,160 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 703, seed 1240733539, best lnL -474.500 +Search rep 1 (of 5) generation 400, seed 1800154253, best lnL -474.639 gen current_lnL precision last_tree_imp -703 -474.4997 0.010 272 -800 -474.4937 0.010 272 -900 -474.4913 0.010 272 -1000 -474.4880 0.010 272 -1100 -474.4855 0.010 272 -1200 -474.4847 0.010 272 -1300 -474.4838 0.010 272 -1400 -474.4822 0.010 272 -1500 -474.4804 0.010 272 -1600 -474.4798 0.010 272 -1700 -474.4795 0.010 272 -1800 -474.4790 0.010 272 -1900 -474.4786 0.010 272 -2000 -474.4786 0.010 272 -2100 -474.4782 0.010 272 -2200 -474.4775 0.010 272 -2300 -474.4768 0.010 272 -2400 -474.4764 0.010 272 -2500 -474.4764 0.010 272 -2600 -474.4747 0.010 272 -2700 -474.4736 0.010 272 -2800 -474.4720 0.010 272 -2900 -474.4720 0.010 272 -3000 -474.4652 0.010 272 -3100 -474.4597 0.010 272 -3200 -474.4561 0.010 272 -3300 -474.4551 0.010 272 -3400 -474.4539 0.010 272 -3500 -474.4525 0.010 272 -3600 -474.4521 0.010 272 -3700 -474.4507 0.010 272 -3800 -474.4505 0.010 272 -3900 -474.4503 0.010 272 -4000 -474.4502 0.010 272 -4100 -474.4501 0.010 272 -4200 -474.4492 0.010 272 -4300 -474.4491 0.010 272 -4400 -474.4486 0.010 272 -4500 -474.4484 0.010 272 -4600 -474.4483 0.010 272 -4700 -474.4474 0.010 272 -4800 -474.4471 0.010 272 -4900 -474.4464 0.010 272 -5000 -474.4464 0.010 272 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL +400 -474.6395 0.010 329 +500 -474.1549 0.010 455 +600 -474.1345 0.010 560 +700 -474.0337 0.010 653 +800 -474.0224 0.010 653 +900 -474.0129 0.010 653 +1000 -474.0072 0.010 653 +1100 -474.0048 0.010 653 +1200 -474.0017 0.010 653 +1300 -473.9998 0.010 653 +1400 -473.9960 0.010 653 +1500 -473.9930 0.010 653 +1600 -473.9888 0.010 653 +1700 -473.9875 0.010 653 +1800 -473.9857 0.010 653 +1900 -473.9846 0.010 653 +2000 -473.9839 0.010 653 +2100 -473.9834 0.010 653 +2200 -473.9820 0.010 653 +2300 -473.9814 0.010 653 +2400 -473.9804 0.010 653 +2500 -473.9804 0.010 653 +2600 -473.9801 0.010 653 +2700 -473.9793 0.010 653 +2800 -473.9779 0.010 653 +2900 -473.9777 0.010 653 +3000 -473.9777 0.010 653 +3100 -473.9773 0.010 653 +3200 -473.9772 0.010 653 +3300 -473.9770 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00088 +Current score = -473.9770 +Performing final optimizations... +pass 1 : -473.9770 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -473.9587 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -473.9587 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9562 (branch= 0.0011 subset rates= 0.0014) +pass 5 : -473.9537 (branch= 0.0013 subset rates= 0.0013) +pass 6 : -473.9523 (branch= 0.0010 subset rates= 0.0003) +pass 7 : -473.9516 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -473.9511 (branch= 0.0004 subset rates= 0.0001) +pass 9 : -473.9509 (branch= 0.0002 subset rates= 0.0000) +pass 10: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 11: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9507 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9507 +Time used so far = 0 hours, 0 minutes and 13 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.80 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.650 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.345 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.473 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8071 +gen current_lnL precision last_tree_imp +0 -474.8071 0.010 0 +100 -474.7912 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -474.4455 +Current score = -474.7912 Performing final optimizations... -pass 1 : -474.4455 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -474.4338 (branch= 0.0117 subset rates= 0.0000) -pass 3 : -474.4321 (branch= 0.0017 subset rates= 0.0000) -pass 4 : -474.4313 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -474.4303 (branch= 0.0010 subset rates= 0.0000) -pass 6 : -474.4297 (branch= 0.0006 subset rates= 0.0001) -pass 7 : -474.4294 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -474.4290 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -474.4286 (branch= 0.0004 subset rates= 0.0000) -pass 10: -474.4283 (branch= 0.0002 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: -474.4282 (branch= 0.0000 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 1 : -474.7420 (branch= 0.0493 subset rates= 0.0000) +pass 2 : -474.6787 (branch= 0.0616 subset rates= 0.0017) +pass 3 : -474.6627 (branch= 0.0160 subset rates= 0.0000) +pass 4 : -474.6560 (branch= 0.0067 subset rates= 0.0000) +pass 5 : -474.6542 (branch= 0.0018 subset rates= 0.0000) +pass 6 : -474.6507 (branch= 0.0025 subset rates= 0.0010) +pass 7 : -474.6479 (branch= 0.0013 subset rates= 0.0016) +pass 8 : -474.6467 (branch= 0.0012 subset rates= 0.0000) +pass 9 : -474.6463 (branch= 0.0004 subset rates= 0.0000) +pass 10: -474.6460 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.6459 (branch= 0.0002 subset rates= 0.0000) +pass 12: -474.6457 (branch= 0.0001 subset rates= 0.0001) +pass 13: -474.6457 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.6456 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.6456 (branch= 0.0001 subset rates= 0.0000) +pass 16: -474.6455 (branch= 0.0000 subset rates= 0.0000) +pass 17: -474.6455 (branch= 0.0000 subset rates= 0.0000) +pass 18: -474.6455 (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 +Final score = -474.6455 +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 @@ -19796,9 +18981,9 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.92 + 0.59 2.01 3.00 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 9 branches were collapsed. >>>Terminated Search rep 2 (of 5)<<< @@ -19814,7 +18999,7 @@ same topology, you should assume that they found different topologies. Results: Replicate 1 : -473.9507 (best) -Replicate 2 : -474.4281 (TERMINATED PREMATURELY) +Replicate 2 : -474.6455 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19830,7 +19015,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.349 0.588 2.066 2.804 -rep 2: 4.600 0.588 2.033 2.917 +rep 2: 4.585 0.586 2.014 3.004 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -19848,13 +19033,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j3 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j4 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/garli-2.1' Making install in src make[2]: Entering directory '/build/garli-2.1/src' make[3]: Entering directory '/build/garli-2.1/src' make[3]: Nothing to be done for 'install-data-am'. - /bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' + /usr/bin/mkdir -p '/build/garli-2.1/debian/tmp/usr/bin' /usr/bin/install -c Garli '/build/garli-2.1/debian/tmp/usr/bin' make install-exec-hook make[4]: Entering directory '/build/garli-2.1/src' @@ -19893,8 +19078,8 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: debian/garli/usr/lib/garli/bin/Garli-2.1 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/garli-mpi/usr/lib/garli/bin/Garli-mpi contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin +dpkg-shlibdeps: warning: debian/garli/usr/lib/garli/bin/Garli-2.1 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb dh_gencontrol dh_md5sums @@ -19911,12 +19096,14 @@ 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/28897/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/28897/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/32726 and its subdirectories -I: Current time: Thu May 4 16:39:55 -12 2023 -I: pbuilder-time-stamp: 1683261595 +I: removing directory /srv/workspace/pbuilder/28897 and its subdirectories +I: Current time: Fri May 5 18:59:44 +14 2023 +I: pbuilder-time-stamp: 1683262784