Diff of the two buildlogs: -- --- b1/build.log 2023-05-08 19:08:03.155896965 +0000 +++ b2/build.log 2023-05-08 19:19:39.229371901 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jun 9 13:24:40 -12 2024 -I: pbuilder-time-stamp: 1717982680 +I: Current time: Tue May 9 09:08:05 +14 2023 +I: pbuilder-time-stamp: 1683572885 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/3092069/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1501427/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +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 9 09:08 /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/1501427/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1501427/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='875ce49f59174a78b9922a5471c2aa74' - 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='3092069' - PS1='# ' - PS2='> ' + INVOCATION_ID=ef3285941fec4591aae7438f777f3b98 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1501427 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.079jLp7g/pbuilderrc_kEox --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.079jLp7g/b1 --logfile b1/build.log garli_2.1-7.dsc' - SUDO_GID='110' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.079jLp7g/pbuilderrc_M8YN --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.079jLp7g/b2 --logfile b2/build.log --extrapackages usrmerge garli_2.1-7.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 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 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 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 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 2023 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 2023 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 2023 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 2023 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 2023 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 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 2022 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 2023 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 2023 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 2023 more - -rwsr-xr-x 1 root root 59704 Mar 22 2023 mount - -rwxr-xr-x 1 root root 18744 Mar 22 2023 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 2023 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 2023 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 2023 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 2023 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 2023 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 2022 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/3092069/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 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 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 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 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 00:02 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 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount + -rwxr-xr-x 1 root root 203152 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 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more + -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount + -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint + -rwxr-xr-x 1 root root 142968 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 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed + lrwxrwxrwx 1 root root 9 May 9 09:08 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 00:02 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/1501427/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -285,7 +317,7 @@ Get: 86 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libopenmpi-dev amd64 4.1.4-3+b1 [970 kB] Get: 88 http://deb.debian.org/debian bookworm/main amd64 ncl-tools amd64 2.1.21+git20210811.b1213a7-4 [199 kB] -Fetched 47.0 MB in 1s (60.9 MB/s) +Fetched 47.0 MB in 1s (32.0 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 ... 19596 files and directories currently installed.) @@ -655,8 +687,19 @@ 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/1501427/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/1501427/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 @@ -753,13 +796,13 @@ checking target system type... x86_64-pc-linux-gnu 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 @@ -790,8 +833,8 @@ 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 @@ -828,7 +871,7 @@ config.status: creating config.h config.status: executing depfiles commands dh_auto_build - make -j16 + make -j15 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -849,7 +892,6 @@ 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 mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp garlimain.cpp:434:66: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 434 | outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); | ^~~~~~~~ @@ -882,6 +924,7 @@ | ~~~~~~~~~~~~~~~~~ /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' /usr/include/x86_64-linux-gnu/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 sequencedata.o sequencedata.cpp 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{ @@ -942,13 +985,11 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 tree.h:35, from individual.h:21, from population.h:31, from funcs.h:25, - from funcs.cpp:30: + from configreader.cpp:30: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -958,7 +999,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -982,7 +1023,6 @@ /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 tree.o tree.cpp 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)); @@ -997,9 +1037,16 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1009,7 +1056,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from model.cpp:17: + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1040,6 +1087,7 @@ /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 translatetable.o translatetable.cpp 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; @@ -1047,21 +1095,23 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: + from /usr/include/c++/12/iomanip:40, + from individual.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1099,23 +1149,14 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from individual.cpp:21: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1156,8 +1197,7 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from configreader.cpp:30: + from garlimain.cpp:40: reconnode.h:58:25: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1167,7 +1207,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -1183,29 +1223,58 @@ /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) + | ^~~~~~~ +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 std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from garlimain.cpp:46: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from tree.h:24: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from model.cpp:17: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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:65:41: warning: 'template struct std::binary_function' is deprecated [-Wdeprecated-declarations] 65 | class DistEqualsWithinCutSubtree:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1218,13 +1287,6 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -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 '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)); @@ -1247,31 +1309,11 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -1312,6 +1354,46 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +In file included from tree.h:35, + from individual.h:21, + from population.h:31, + from population.cpp:45: +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 population.cpp:23: +/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; @@ -1319,11 +1401,27 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: +reconnode.h: In member function 'void ReconList::AddNode(int, int, float, bool)': +reconnode.h:202:53: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = NodeEquals; _Tp = int]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] + 202 | if(find_if(l.begin(),l.end(),bind2nd(NodeEquals(), nn)) != l.end()) return; + | ~~~~~~~^~~~~~~~~~~~~~~~~~ +/usr/include/c++/12/backward/binders.h:172:5: note: declared here + 172 | bind2nd(const _Operation& __fn, const _Tp& __x) + | ^~~~~~~ +In file included from population.cpp:49: funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/refwrap.h:39, - from /usr/include/c++/12/vector:66, - from population.cpp:23: -/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) - | ^~~~~~~ -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 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 population.cpp:49: -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/bits/stl_tree.h:65, - from /usr/include/c++/12/map:60, - from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, - from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, - from mpitrick.cpp:20: -/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) - | ^~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/bits/stl_tree.h:65, + from /usr/include/c++/12/map:60, + from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:42, + from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887, + from mpitrick.cpp:20: +/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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ @@ -2255,7 +2296,7 @@ /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 translatetable.o translatetable.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp 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); @@ -2276,17 +2317,15 @@ from individual.h:21, from population.h:31, from funcs.h:25, - from adaptation.cpp:25: + from individual.cpp:28: 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/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from adaptation.cpp:18: + from /usr/include/c++/12/iomanip:40, + from individual.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2324,12 +2363,16 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2339,7 +2382,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from population.h:23: + from configreader.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2355,19 +2398,42 @@ /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 file included from tree.h:35, from individual.h:21, from population.h:31, - from funcs.h:25, - from individual.cpp:28: + from garlimain.cpp:40: 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/string:48, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/iomanip:40, - from individual.cpp:21: + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2398,6 +2464,52 @@ /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) + | ^~~~~~~ +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 +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] + 58 | class DistEquals:public binary_function{ + | ^~~~~~~~~~~~~~~ +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from model.cpp:17: +/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)); @@ -2420,25 +2532,16 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/12/bits/refwrap.h:39, from /usr/include/c++/12/vector:66, - from tree.h:24: + from population.cpp:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2476,10 +2579,7 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': -funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] - 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2498,7 +2598,7 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from configreader.cpp:21: + from population.h:23: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2536,29 +2636,14 @@ /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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from population.h:23: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.h:24: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2599,13 +2684,18 @@ In file included from tree.h:35, from individual.h:21, from population.h:31, - from population.cpp:45: + from funcs.h:25, + from adaptation.cpp:25: 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 population.cpp:23: +In file included from /usr/include/c++/12/string:48, + from /usr/include/c++/12/bits/locale_classes.h:40, + from /usr/include/c++/12/bits/ios_base.h:41, + from /usr/include/c++/12/ios:42, + from /usr/include/c++/12/ostream:38, + from /usr/include/c++/12/iostream:39, + from adaptation.cpp:18: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2615,6 +2705,10 @@ /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] 72 | class NodeEquals:public binary_function{ | ^~~~~~~~~~~~~~~ @@ -2643,29 +2737,69 @@ /usr/include/c++/12/backward/binders.h:172:5: note: declared here 172 | bind2nd(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ -In file included from garlimain.cpp:46: +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 struct std::binary_function' is deprecated [-Wdeprecated-declarations] 58 | class DistEquals:public binary_function{ | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/string:48, - from /usr/include/c++/12/bits/locale_classes.h:40, - from /usr/include/c++/12/bits/ios_base.h:41, - from /usr/include/c++/12/ios:42, - from /usr/include/c++/12/ostream:38, - from /usr/include/c++/12/iostream:39, - from model.cpp:17: +In file included from /usr/include/c++/12/bits/refwrap.h:39, + from /usr/include/c++/12/vector:66, + from tree.cpp:21: /usr/include/c++/12/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ @@ -2703,11 +2837,10 @@ /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 treenode.o treenode.cpp -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result] - 1390 | fscanf(inf, "%d %d", &num_taxa, &num_chars); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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); + | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 271 | fread((char *) this, 1, scalarSize, in); @@ -2769,44 +2902,10 @@ adaptation.cpp:305:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 305 | fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::string&)': -configreader.cpp:602:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 602 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] - 605 | fread(&ch, sizeof(char), 1, file); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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); - | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +funcs.h: In function 'void ArrayMultiply(FLOAT_TYPE*, const FLOAT_TYPE*, int)': +funcs.h:170:26: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister] + 170 | for(register int i=0;i struct std::binary_function' is deprecated [-Wdeprecated-declarations] - 58 | class DistEquals:public binary_function{ - | ^~~~~~~~~~~~~~~ -In file included from /usr/include/c++/12/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) - | ^~~~~~~ -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 -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;idlen, sizeof(FLOAT_TYPE), 1, in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:906, + from configreader.cpp:18: +In function 'int sprintf(char*, const char*, ...)', + inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/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, @@ -3049,6 +3028,21 @@ /usr/include/x86_64-linux-gnu/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/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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/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, @@ -3057,7 +3051,9 @@ from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, - from datamatr.cpp:20: + from model.h:25, + from clamanager.h:25, + from condlike.cpp:22: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3071,8 +3067,9 @@ /usr/include/x86_64-linux-gnu/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/ncl/ncl.h:27, - from garlireader.cpp:41: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3105,6 +3102,25 @@ 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/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, from translatetable.h:24, from translatetable.cpp:19: In function 'int sprintf(char*, const char*, ...)', @@ -3155,9 +3171,36 @@ 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: + 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/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] + 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 31 | __glibc_objsize (__s), __fmt, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 32 | __va_arg_pack ()); + | ~~~~~~~~~~~~~~~~~ +/usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: note: in a call to built-in function 'int __builtin_sprintf(char*, const char*, ...)' +/usr/include/x86_64-linux-gnu/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 /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 datamatr.cpp:20: In function 'int sprintf(char*, const char*, ...)', inlined from 'ErrorException::ErrorException(const char*, ...)' at errorexception.h:97:12: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:34: warning: argument 1 null where non-null expected [-Wnonnull] @@ -3259,7 +3302,7 @@ # 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 -j16 check "TESTSUITEFLAGS=-j16 --verbose" VERBOSE=1 + make -j15 check "TESTSUITEFLAGS=-j15 --verbose" VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -5779,7 +5822,7 @@ 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 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5929,7 +5972,7 @@ 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 0 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6072,7 +6115,7 @@ 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 ... ####################################################### @@ -6226,7 +6269,7 @@ 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 13 seconds +Time used = 0 hours, 0 minutes and 28 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6378,7 +6421,7 @@ 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 9 seconds +Time used = 0 hours, 0 minutes and 18 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6582,7 +6625,7 @@ pass 80: -3350.2333 (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 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6790,7 +6833,7 @@ pass 76: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 3 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -6952,7 +6995,7 @@ pass 10: -13930.5180 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13930.5180 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7276,7 +7319,7 @@ pass 17: -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 5 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -7530,7 +7573,7 @@ pass 35: -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 3 seconds +Time used = 0 hours, 0 minutes and 7 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -9500,7 +9543,7 @@ pass 497: -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 3 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -9764,7 +9807,7 @@ pass 373: -208.1243 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.1243 -Time used = 0 hours, 0 minutes and 4 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10056,7 +10099,7 @@ pass 509: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 4 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -10349,7 +10392,7 @@ pass 491: -208.3585 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -208.3585 -Time used = 0 hours, 0 minutes and 3 seconds +Time used = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -13065,7 +13108,6 @@ Optimizing parameters... improved 0.159 lnL Optimizing branchlengths... improved 0.317 lnL 900 -88.9507 0.010 879 -1000 -88.8871 0.010 879 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13162,11 +13204,13 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1049, seed 2111262234, best lnL -88.870 +Bootstrap rep 1 (of 1) generation 939, seed 1220911760, best lnL -88.930 gen current_lnL precision last_tree_imp -1049 -88.8695 0.010 879 +939 -88.9303 0.010 879 +1000 -88.8871 0.010 879 +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 @@ -13178,37 +13222,41 @@ 0.0826 0.0496 0.0579 0.0083 0.0331 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 0.9149 + 0.9045 with an invariant (invariable) site category, proportion estimated 0.1355 Substitution rate categories under this model: rate proportion 0.0000 0.1355 - 0.1694 0.2882 - 0.6887 0.2882 - 2.1419 0.2882 + 0.1669 0.2882 + 0.6855 0.2882 + 2.1476 0.2882 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 2 branches were collapsed. + 1 branches were collapsed. + + +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 : -88.8695 +Replicate 1 : -88.8871 Parameter estimates: alpha pinv -rep 1: 0.915 0.136 +rep 1: 0.904 0.136 Treelengths: TL -rep 1: 2.362 +rep 1: 2.441 Saving best tree to bootstrap file ch.a.G3.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/a.G4.conf @@ -13335,7 +13383,6 @@ Optimization precision reduced Optimizing parameters... improved 0.386 lnL Optimizing branchlengths... improved 0.390 lnL -700 -110.8142 0.010 615 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13422,9 +13469,10 @@ STARTING RUN Restarting from checkpoint... - generation 799, seed 438163445, best lnL -110.564 + generation 607, seed 160549652, best lnL -110.910 gen current_lnL precision last_tree_imp -799 -110.5642 0.010 707 +607 -110.9098 0.010 607 +700 -110.8142 0.010 615 800 -110.5642 0.010 707 900 -110.5555 0.010 707 1000 -110.5066 0.010 707 @@ -13613,12 +13661,6 @@ 1700 -111.6818 0.010 563 1800 -111.6818 0.010 563 1900 -111.6818 0.010 563 -2000 -111.6817 0.010 563 -2100 -111.6817 0.010 563 -2200 -111.6817 0.010 563 -2300 -111.6817 0.010 563 -2400 -111.6817 0.010 563 -2500 -111.6817 0.010 563 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13704,9 +13746,9 @@ STARTING RUN Restarting from checkpoint... - generation 2511, seed 257275133, best lnL -111.682 + generation 1962, seed 1306271184, best lnL -111.682 gen current_lnL precision last_tree_imp -2511 -111.6817 0.010 563 +1962 -111.6817 0.010 563 MODEL REPORT - Parameter values are FINAL Model 1 @@ -13722,7 +13764,7 @@ 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.a.sitelikes.log ... @@ -13737,7 +13779,7 @@ Treelengths: TL -rep 1: 2.604 +rep 1: 2.605 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 @@ -13871,11 +13913,6 @@ 50 -205.6175 0.500 18 60 -205.5990 0.500 53 70 -205.5741 0.500 53 -80 -205.4022 0.500 76 -90 -205.3871 0.500 76 -100 -205.3829 0.500 76 -110 -205.3431 0.500 106 -120 -205.3431 0.500 106 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13962,11 +13999,15 @@ STARTING RUN Restarting from checkpoint... - generation 122, seed 213781473, best lnL -205.296 + generation 75, seed 618198881, best lnL -205.501 gen current_lnL precision last_tree_imp -122 -205.2960 0.500 121 +75 -205.5007 0.500 53 +80 -205.4022 0.500 76 +90 -205.3871 0.500 76 +100 -205.3829 0.500 76 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates @@ -13998,12 +14039,17 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.c.M3x2.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 : -205.2960 +Replicate 1 : -205.3829 Parameter estimates: w(0) p(0) w(1) p(1) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) @@ -14011,11 +14057,13 @@ Treelengths: TL -rep 1: 7.779 +rep 1: 7.371 Saving final tree from best search rep (#1) to ch.c.M3x2.best.tre Inferring internal state probabilities on best tree... saving to file ch.c.M3x2.internalstates.log +WARNING: Internal states inferred on tree from prematurely terminated search + ####################################################### TREEFILES PASS Running checkpoint test ./check/c.conf @@ -14148,10 +14196,6 @@ 50 -195.2139 0.500 0 60 -195.1631 0.500 0 70 -195.0044 0.500 0 -80 -194.9479 0.500 0 -90 -194.9093 0.500 0 -100 -194.9093 0.500 0 -110 -194.8988 0.500 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14239,16 +14283,20 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 119, seed 612438734, best lnL -194.899 +Bootstrap rep 1 (of 1) generation 74, seed 2116197142, best lnL -194.972 gen current_lnL precision last_tree_imp -119 -194.8988 0.500 0 +74 -194.9722 0.500 0 +80 -194.9479 0.500 0 +90 -194.9093 0.500 0 +100 -194.9093 0.500 0 +NOTE: ****Specified generation limit (100) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 61 (codon data, standard code) One estimated dN/dS ratio (aka omega) = 0.120505 Nucleotide Relative Rate Matrix Assumed by Codon Model: 6 rates - AC = 1.637, AG = 5.749, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 + AC = 1.637, AG = 5.679, AT = 0.011, CG = 4.174, CT = 2.324, GT = 1.000 Equilibrium State Frequencies: empirical values calculated by F3x4 method (fixed) (AAA, AAC, AAG, AAT, ACA, ... etc) @@ -14272,15 +14320,19 @@ No branches were short enough to be collapsed. +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 : -194.8988 +Replicate 1 : -194.9093 Parameter estimates: w(0) p(0) r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) -rep 1: 0.121 1.000 1.637 5.749 0.01146 4.174 2.324 1 +rep 1: 0.121 1.000 1.637 5.679 0.01146 4.174 2.324 1 Treelengths: TL @@ -14288,7 +14340,7 @@ Saving best tree to bootstrap file ch.c.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/g.dnaBnoZ.conf @@ -14456,12 +14508,6 @@ 1500 -3352.2780 0.010 0 1600 -3352.1759 0.010 0 1700 -3352.1636 0.010 0 -1800 -3352.0835 0.010 0 -1900 -3351.7358 0.010 0 -2000 -3351.6699 0.010 0 -2100 -3351.4842 0.010 0 -2200 -3351.3005 0.010 0 -2300 -3351.2529 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14565,84 +14611,75 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 2346, seed 1993999723, best lnL -3351.245 +Search rep 1 (of 2) generation 1733, seed 2022945329, best lnL -3352.084 gen current_lnL precision last_tree_imp -2346 -3351.2453 0.010 0 +1733 -3352.0843 0.010 0 +1800 -3352.0835 0.010 0 +1900 -3351.7358 0.010 0 +2000 -3351.6699 0.010 0 +2100 -3351.4842 0.010 0 +2200 -3351.3005 0.010 0 +2300 -3351.2529 0.010 0 2400 -3351.2174 0.010 0 2500 -3351.1254 0.010 0 2600 -3351.0627 0.010 0 2700 -3351.0624 0.010 0 -2800 -3351.0570 0.010 0 -2900 -3351.0136 0.010 0 -3000 -3351.0136 0.010 0 -3100 -3351.0009 0.010 0 -3200 -3350.9820 0.010 0 -3300 -3350.9796 0.010 0 -3400 -3350.9765 0.010 0 -3500 -3350.9763 0.010 0 -3600 -3350.9757 0.010 0 -3700 -3350.9427 0.010 0 -3800 -3350.9285 0.010 0 -3900 -3350.8683 0.010 0 -4000 -3350.8683 0.010 0 -4100 -3350.8586 0.010 0 -4200 -3350.8530 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3350.8530 +Current score = -3351.0624 Performing final optimizations... -pass 1 : -3350.8138 (branch= 0.0000 alpha= 0.0000 pinv= 0.0092 eq freqs= 0.0059 rel rates= 0.0217 subset rates= 0.0025) -pass 2 : -3350.7474 (branch= 0.0053 alpha= 0.0108 pinv= 0.0175 eq freqs= 0.0000 rel rates= 0.0328 subset rates= 0.0000) -pass 3 : -3350.6833 (branch= 0.0075 alpha= 0.0170 pinv= 0.0153 eq freqs= 0.0035 rel rates= 0.0193 subset rates= 0.0015) -pass 4 : -3350.6311 (branch= 0.0054 alpha= 0.0132 pinv= 0.0145 eq freqs= 0.0000 rel rates= 0.0178 subset rates= 0.0013) -pass 5 : -3350.5847 (branch= 0.0045 alpha= 0.0130 pinv= 0.0133 eq freqs= 0.0000 rel rates= 0.0156 subset rates= 0.0000) -pass 6 : -3350.5425 (branch= 0.0013 alpha= 0.0126 pinv= 0.0119 eq freqs= 0.0003 rel rates= 0.0144 subset rates= 0.0016) -pass 7 : -3350.5066 (branch= 0.0021 alpha= 0.0110 pinv= 0.0109 eq freqs= 0.0001 rel rates= 0.0117 subset rates= 0.0000) -pass 8 : -3350.4737 (branch= 0.0006 alpha= 0.0101 pinv= 0.0099 eq freqs= 0.0000 rel rates= 0.0112 subset rates= 0.0012) -pass 9 : -3350.4452 (branch= 0.0011 alpha= 0.0092 pinv= 0.0090 eq freqs= 0.0000 rel rates= 0.0093 subset rates= 0.0000) -pass 10: -3350.4198 (branch= 0.0002 alpha= 0.0085 pinv= 0.0081 eq freqs= 0.0000 rel rates= 0.0086 subset rates= 0.0000) -pass 11: -3350.3967 (branch= 0.0001 alpha= 0.0080 pinv= 0.0072 eq freqs= 0.0000 rel rates= 0.0077 subset rates= 0.0000) -pass 12: -3350.3762 (branch= 0.0000 alpha= 0.0073 pinv= 0.0065 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) -pass 13: -3350.3581 (branch= 0.0000 alpha= 0.0065 pinv= 0.0058 eq freqs= 0.0000 rel rates= 0.0058 subset rates= 0.0000) -pass 14: -3350.3421 (branch= 0.0000 alpha= 0.0058 pinv= 0.0051 eq freqs= 0.0000 rel rates= 0.0050 subset rates= 0.0000) -pass 15: -3350.3280 (branch= 0.0000 alpha= 0.0052 pinv= 0.0046 eq freqs= 0.0000 rel rates= 0.0044 subset rates= 0.0000) -pass 16: -3350.3156 (branch= 0.0000 alpha= 0.0046 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0037 subset rates= 0.0000) -pass 17: -3350.3047 (branch= 0.0000 alpha= 0.0040 pinv= 0.0036 eq freqs= 0.0000 rel rates= 0.0032 subset rates= 0.0000) -pass 18: -3350.2951 (branch= 0.0000 alpha= 0.0036 pinv= 0.0032 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) -pass 19: -3350.2868 (branch= 0.0000 alpha= 0.0031 pinv= 0.0028 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) -pass 20: -3350.2795 (branch= 0.0000 alpha= 0.0027 pinv= 0.0024 eq freqs= 0.0000 rel rates= 0.0021 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2434 (branch= 0.0000 alpha= 0.0137 pinv= 0.0124 eq freqs= 0.0000 rel rates= 0.0100 subset rates= 0.0000) +pass 1 : -3350.9644 (branch= 0.0000 alpha= 0.0000 pinv= 0.0249 eq freqs= 0.0169 rel rates= 0.0509 subset rates= 0.0054) +pass 2 : -3350.8700 (branch= 0.0063 alpha= 0.0115 pinv= 0.0173 eq freqs= 0.0000 rel rates= 0.0593 subset rates= 0.0000) +pass 3 : -3350.7862 (branch= 0.0125 alpha= 0.0146 pinv= 0.0159 eq freqs= 0.0000 rel rates= 0.0383 subset rates= 0.0025) +pass 4 : -3350.7202 (branch= 0.0049 alpha= 0.0137 pinv= 0.0146 eq freqs= 0.0009 rel rates= 0.0308 subset rates= 0.0011) +pass 5 : -3350.6627 (branch= 0.0042 alpha= 0.0126 pinv= 0.0135 eq freqs= 0.0000 rel rates= 0.0272 subset rates= 0.0000) +pass 6 : -3350.6100 (branch= 0.0002 alpha= 0.0130 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.0260 subset rates= 0.0009) +pass 7 : -3350.5636 (branch= 0.0024 alpha= 0.0114 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0212 subset rates= 0.0000) +pass 8 : -3350.5230 (branch= 0.0004 alpha= 0.0103 pinv= 0.0101 eq freqs= 0.0000 rel rates= 0.0186 subset rates= 0.0012) +pass 9 : -3350.4874 (branch= 0.0012 alpha= 0.0095 pinv= 0.0093 eq freqs= 0.0001 rel rates= 0.0156 subset rates= 0.0000) +pass 10: -3350.4562 (branch= 0.0002 alpha= 0.0087 pinv= 0.0083 eq freqs= 0.0000 rel rates= 0.0139 subset rates= 0.0000) +pass 11: -3350.4281 (branch= 0.0001 alpha= 0.0083 pinv= 0.0075 eq freqs= 0.0000 rel rates= 0.0123 subset rates= 0.0000) +pass 12: -3350.4033 (branch= 0.0000 alpha= 0.0075 pinv= 0.0067 eq freqs= 0.0000 rel rates= 0.0105 subset rates= 0.0000) +pass 13: -3350.3815 (branch= 0.0000 alpha= 0.0067 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0090 subset rates= 0.0000) +pass 14: -3350.3624 (branch= 0.0000 alpha= 0.0060 pinv= 0.0054 eq freqs= 0.0000 rel rates= 0.0078 subset rates= 0.0000) +pass 15: -3350.3455 (branch= 0.0000 alpha= 0.0054 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0067 subset rates= 0.0000) +pass 16: -3350.3308 (branch= 0.0000 alpha= 0.0048 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0057 subset rates= 0.0000) +pass 17: -3350.3179 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0049 subset rates= 0.0000) +pass 18: -3350.3066 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0042 subset rates= 0.0000) +pass 19: -3350.2968 (branch= 0.0000 alpha= 0.0033 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) +pass 20: -3350.2883 (branch= 0.0000 alpha= 0.0029 pinv= 0.0026 eq freqs= 0.0000 rel rates= 0.0031 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2457 (branch= 0.0000 alpha= 0.0143 pinv= 0.0130 eq freqs= 0.0000 rel rates= 0.0152 subset rates= 0.0000) optimization up to ... -pass 40: -3350.2354 (branch= 0.0000 alpha= 0.0029 pinv= 0.0027 eq freqs= 0.0000 rel rates= 0.0024 subset rates= 0.0000) +pass 40: -3350.2361 (branch= 0.0000 alpha= 0.0031 pinv= 0.0029 eq freqs= 0.0000 rel rates= 0.0036 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2338 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0005 subset rates= 0.0000) +pass 50: -3350.2341 (branch= 0.0000 alpha= 0.0006 pinv= 0.0005 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2335 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0001 subset rates= 0.0000) +pass 60: -3350.2337 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 62: -3350.2335 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 66: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -3350.2335 +Final score = -3350.2337 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.113, AG = 10.403, AT = 2.686, CG = 0.001, CT = 21.871, GT = 1.000 + AC = 3.112, AG = 10.397, AT = 2.684, CG = 0.001, CT = 21.845, 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 - 0.5774 + 0.5786 with an invariant (invariable) site category, proportion estimated - 0.3655 + 0.3659 Substitution rate categories under this model: rate proportion - 0.0000 0.3655 - 0.0485 0.1586 - 0.2995 0.1586 - 0.8693 0.1586 - 2.7827 0.1586 + 0.0000 0.3659 + 0.0487 0.1585 + 0.3002 0.1585 + 0.8700 0.1585 + 2.7811 0.1585 Model 2 Number of states = 2 (binary data) @@ -14667,20 +14704,20 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2335 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2337 (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: 3.113 10.4 2.686 0.001 21.87 1 0.333 0.222 0.157 0.288 0.577 0.366 +rep 1: 3.112 10.4 2.684 0.001 21.85 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: 0.788 1.820 0.180 +rep 1: 0.787 1.820 0.180 Saving final tree from best search rep (#1) to ch.g.dnaBnoZ.best.tre ####################################################### @@ -14831,14 +14868,6 @@ 300 -3324.3007 0.500 1 400 -3323.9848 0.500 1 500 -3323.6818 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 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14939,77 +14968,81 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 1007, seed 675618299, best lnL -3320.967 +Search rep 1 (of 2) generation 594, seed 485400439, best lnL -3323.379 gen current_lnL precision last_tree_imp -1007 -3320.9667 0.255 1 +594 -3323.3791 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 1100 -3320.8654 0.255 1 Optimization precision reduced Optimizing parameters... improved 0.580 lnL Optimizing branchlengths... improved 0.061 lnL 1200 -3320.1418 0.010 1 1300 -3320.0829 0.010 1 -1400 -3320.0708 0.010 1 -1500 -3320.0228 0.010 1 -1600 -3320.0186 0.010 1 -1700 -3320.0155 0.010 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3320.0124 +Current score = -3320.0829 Performing final optimizations... -pass 1 : -3319.5750 (branch= 0.0076 alpha= 0.0000 pinv= 0.0143 eq freqs= 0.0000 rel rates= 0.3675 ins/del rates= 0.0479) -pass 2 : -3319.2712 (branch= 0.0360 alpha= 0.0186 pinv= 0.0151 eq freqs= 0.0097 rel rates= 0.2156 ins/del rates= 0.0087) -pass 3 : -3319.0380 (branch= 0.0344 alpha= 0.0129 pinv= 0.0151 eq freqs= 0.0000 rel rates= 0.1632 ins/del rates= 0.0074) -pass 4 : -3318.8586 (branch= 0.0166 alpha= 0.0111 pinv= 0.0147 eq freqs= 0.0019 rel rates= 0.1305 ins/del rates= 0.0046) -pass 5 : -3318.6983 (branch= 0.0142 alpha= 0.0117 pinv= 0.0139 eq freqs= 0.0011 rel rates= 0.1142 ins/del rates= 0.0052) -pass 6 : -3318.5717 (branch= 0.0081 alpha= 0.0105 pinv= 0.0131 eq freqs= 0.0005 rel rates= 0.0910 ins/del rates= 0.0033) -pass 7 : -3318.4622 (branch= 0.0059 alpha= 0.0103 pinv= 0.0122 eq freqs= 0.0004 rel rates= 0.0781 ins/del rates= 0.0025) -pass 8 : -3318.3685 (branch= 0.0037 alpha= 0.0100 pinv= 0.0113 eq freqs= 0.0002 rel rates= 0.0668 ins/del rates= 0.0016) -pass 9 : -3318.2883 (branch= 0.0028 alpha= 0.0091 pinv= 0.0105 eq freqs= 0.0001 rel rates= 0.0565 ins/del rates= 0.0012) -pass 10: -3318.2195 (branch= 0.0019 alpha= 0.0090 pinv= 0.0096 eq freqs= 0.0001 rel rates= 0.0474 ins/del rates= 0.0008) -pass 11: -3318.1608 (branch= 0.0012 alpha= 0.0084 pinv= 0.0087 eq freqs= 0.0001 rel rates= 0.0397 ins/del rates= 0.0005) -pass 12: -3318.1104 (branch= 0.0008 alpha= 0.0078 pinv= 0.0079 eq freqs= 0.0001 rel rates= 0.0334 ins/del rates= 0.0003) -pass 13: -3318.0677 (branch= 0.0005 alpha= 0.0074 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0274 ins/del rates= 0.0002) -pass 14: -3318.0309 (branch= 0.0003 alpha= 0.0067 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0230 ins/del rates= 0.0001) -pass 15: -3317.9989 (branch= 0.0002 alpha= 0.0061 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0197 ins/del rates= 0.0001) -pass 16: -3317.9711 (branch= 0.0001 alpha= 0.0055 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0168 ins/del rates= 0.0000) -pass 17: -3317.9469 (branch= 0.0001 alpha= 0.0050 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0144 ins/del rates= 0.0000) -pass 18: -3317.9258 (branch= 0.0001 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0123 ins/del rates= 0.0000) -pass 19: -3317.9075 (branch= 0.0000 alpha= 0.0040 pinv= 0.0037 eq freqs= 0.0000 rel rates= 0.0105 ins/del rates= 0.0000) -pass 20: -3317.8916 (branch= 0.0000 alpha= 0.0036 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0090 ins/del rates= 0.0000) - optimization up to ... -pass 30: -3317.8116 (branch= 0.0001 alpha= 0.0190 pinv= 0.0175 eq freqs= 0.0001 rel rates= 0.0433 ins/del rates= 0.0000) - optimization up to ... -pass 40: -3317.7926 (branch= 0.0001 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0100 ins/del rates= 0.0000) +pass 1 : -3319.6953 (branch= 0.0239 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0001 rel rates= 0.3239 ins/del rates= 0.0397) +pass 2 : -3319.4250 (branch= 0.0347 alpha= 0.0000 pinv= 0.0080 eq freqs= 0.0000 rel rates= 0.2203 ins/del rates= 0.0073) +pass 3 : -3319.1772 (branch= 0.0268 alpha= 0.0098 pinv= 0.0163 eq freqs= 0.0039 rel rates= 0.1825 ins/del rates= 0.0085) +pass 4 : -3318.9769 (branch= 0.0190 alpha= 0.0112 pinv= 0.0159 eq freqs= 0.0007 rel rates= 0.1484 ins/del rates= 0.0051) +pass 5 : -3318.7978 (branch= 0.0146 alpha= 0.0138 pinv= 0.0152 eq freqs= 0.0024 rel rates= 0.1278 ins/del rates= 0.0052) +pass 6 : -3318.6546 (branch= 0.0087 alpha= 0.0115 pinv= 0.0143 eq freqs= 0.0009 rel rates= 0.1042 ins/del rates= 0.0036) +pass 7 : -3318.5346 (branch= 0.0064 alpha= 0.0114 pinv= 0.0133 eq freqs= 0.0003 rel rates= 0.0858 ins/del rates= 0.0027) +pass 8 : -3318.4305 (branch= 0.0043 alpha= 0.0108 pinv= 0.0124 eq freqs= 0.0002 rel rates= 0.0745 ins/del rates= 0.0019) +pass 9 : -3318.3418 (branch= 0.0031 alpha= 0.0101 pinv= 0.0115 eq freqs= 0.0001 rel rates= 0.0624 ins/del rates= 0.0013) +pass 10: -3318.2653 (branch= 0.0021 alpha= 0.0099 pinv= 0.0112 eq freqs= 0.0001 rel rates= 0.0523 ins/del rates= 0.0009) +pass 11: -3318.1999 (branch= 0.0014 alpha= 0.0094 pinv= 0.0103 eq freqs= 0.0001 rel rates= 0.0436 ins/del rates= 0.0006) +pass 12: -3318.1445 (branch= 0.0009 alpha= 0.0087 pinv= 0.0088 eq freqs= 0.0001 rel rates= 0.0365 ins/del rates= 0.0004) +pass 13: -3318.0968 (branch= 0.0006 alpha= 0.0081 pinv= 0.0080 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0003) +pass 14: -3318.0563 (branch= 0.0004 alpha= 0.0075 pinv= 0.0072 eq freqs= 0.0001 rel rates= 0.0251 ins/del rates= 0.0002) +pass 15: -3318.0212 (branch= 0.0002 alpha= 0.0069 pinv= 0.0065 eq freqs= 0.0001 rel rates= 0.0213 ins/del rates= 0.0001) +pass 16: -3317.9907 (branch= 0.0002 alpha= 0.0062 pinv= 0.0059 eq freqs= 0.0000 rel rates= 0.0181 ins/del rates= 0.0001) +pass 17: -3317.9641 (branch= 0.0001 alpha= 0.0056 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0155 ins/del rates= 0.0000) +pass 18: -3317.9410 (branch= 0.0001 alpha= 0.0051 pinv= 0.0047 eq freqs= 0.0000 rel rates= 0.0132 ins/del rates= 0.0000) +pass 19: -3317.9208 (branch= 0.0000 alpha= 0.0045 pinv= 0.0042 eq freqs= 0.0000 rel rates= 0.0113 ins/del rates= 0.0000) +pass 20: -3317.9032 (branch= 0.0000 alpha= 0.0041 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0097 ins/del rates= 0.0000) + optimization up to ... +pass 30: -3317.8145 (branch= 0.0001 alpha= 0.0219 pinv= 0.0201 eq freqs= 0.0001 rel rates= 0.0464 ins/del rates= 0.0000) + optimization up to ... +pass 40: -3317.7932 (branch= 0.0001 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0000 rel rates= 0.0107 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7882 (branch= 0.0000 alpha= 0.0010 pinv= 0.0009 eq freqs= 0.0000 rel rates= 0.0024 ins/del rates= 0.0000) +pass 50: -3317.7884 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0026 ins/del rates= 0.0000) optimization up to ... -pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0005 ins/del rates= 0.0000) +pass 60: -3317.7873 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0006 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7870 (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= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) optimization up to ... -pass 72: -3317.7870 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 75: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001 ins/del rates= 0.0000) Looking for minimum length branches... -Final score = -3317.7870 -Time used so far = 0 hours, 0 minutes and 12 seconds +Final score = -3317.7871 +Time used so far = 0 hours, 0 minutes and 13 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.067, AG = 10.274, AT = 2.660, CG = 0.001, CT = 21.559, GT = 1.000 + AC = 3.069, AG = 10.273, AT = 2.658, CG = 0.001, CT = 21.562, 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 - 0.5749 + 0.5747 with an invariant (invariable) site category, proportion estimated - 0.3613 + 0.3612 Substitution rate categories under this model: rate proportion - 0.0000 0.3613 - 0.0480 0.1597 - 0.2980 0.1597 - 0.8679 0.1597 - 2.7861 0.1597 + 0.0000 0.3612 + 0.0479 0.1597 + 0.2979 0.1597 + 0.8678 0.1597 + 2.7863 0.1597 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -15035,13 +15068,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3317.7870 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3317.7871 (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: 3.067 10.27 2.66 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.069 10.27 2.658 0.001 21.56 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -15051,7 +15084,7 @@ Treelengths: TL -rep 1: 1.418 +rep 1: 1.419 Saving final tree from best search rep (#1) to ch.g.dnaMix.best.tre ####################################################### @@ -15210,8 +15243,6 @@ 8600 -210.0896 0.010 1104 8800 -210.0544 0.010 1104 9000 -210.0431 0.010 1104 -9200 -209.9790 0.010 1104 -9400 -209.9602 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15291,9 +15322,14 @@ STARTING RUN Restarting from checkpoint... - generation 9557, seed 403411942, best lnL -209.950 + generation 9069, seed 1449110123, best lnL -210.000 gen current_lnL precision last_tree_imp -9557 -209.9503 0.010 1104 +9069 -210.0002 0.010 1104 +9100 -209.9813 0.010 1104 +9200 -209.9790 0.010 1104 +9300 -209.9616 0.010 1104 +9400 -209.9602 0.010 1104 +9500 -209.9581 0.010 1104 9600 -209.9463 0.010 1104 Reached termination condition! last topological improvement at gen 1104 @@ -15501,60 +15537,15 @@ 8800 -164.0451 0.010 7540 9000 -163.8875 0.010 7540 9200 -163.8770 0.010 7540 -9400 -163.8420 0.010 7540 -9600 -163.7589 0.010 7540 -9800 -163.7099 0.010 7540 -10000 -163.6726 0.010 7540 - Optimizing parameters... improved 1.625 lnL - Optimizing branchlengths... improved 0.035 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 = 0.657, AG = 11.198, AT = 2.636, CG = 4.226, CT = 36.018, GT = 1.000 - Equilibrium State Frequencies: estimated - (ACGT) 0.1301 0.4168 0.2379 0.2153 - Rate Heterogeneity Model: - 4 discrete gamma distributed rate categories, alpha param estimated - 520.4918 - with an invariant (invariable) site category, proportion estimated - 0.3438 - Substitution rate categories under this model: - rate proportion - 0.0000 0.3438 - 0.9448 0.1641 - 0.9852 0.1641 - 1.0137 0.1641 - 1.0563 0.1641 - -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 3 branches were collapsed. - - -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 : -162.0129 - -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: 0.6567 11.2 2.636 4.226 36.02 1 0.130 0.417 0.238 0.215 520.492 0.344 - -Treelengths: - TL -rep 1: 2.894 +NOTE: ****Specified time limit (5 seconds) reached... -Saving best tree to bootstrap file ch.n.G4.boot.tre +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. -WARNING: Tree from prematurely terminated search saved to bootstrap file -####################################################### Running GARLI Version 2.1. () ->Single processor version for 64-bit OS<- ############################################################## @@ -15626,11 +15617,21 @@ Subset 1: Random seed for bootstrap reweighting: 42 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 10001, seed 258537382, best lnL -162.013 +Bootstrap rep 1 (of 1) generation 9362, seed 1519852820, best lnL -163.842 gen current_lnL precision last_tree_imp -10001 -162.0129 0.010 7540 +9362 -163.8422 0.010 7540 +9400 -163.8420 0.010 7540 +9500 -163.7908 0.010 7540 +9600 -163.7589 0.010 7540 +9700 -163.7261 0.010 7540 +9800 -163.7099 0.010 7540 +9900 -163.7095 0.010 7540 +10000 -163.6726 0.010 7540 + Optimizing parameters... improved 1.625 lnL + Optimizing branchlengths... improved 0.035 lnL +NOTE: ****Specified generation limit (10000) reached... -MODEL REPORT - Parameter values are FINAL +MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates @@ -15654,6 +15655,10 @@ 3 branches were collapsed. +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). @@ -15670,7 +15675,7 @@ Saving best tree to bootstrap file ch.n.G4.boot.tre ->>>Completed Bootstrap rep 1<<< +WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -16536,14 +16541,6 @@ Optimization precision reduced Optimizing parameters... improved 0.037 lnL Optimizing branchlengths... improved 0.000 lnL -1100 -13370.5869 0.304 0 -1200 -13370.5241 0.304 0 -1300 -13370.5103 0.304 0 -1400 -13370.5063 0.304 0 -1500 -13370.4967 0.304 0 -Optimization precision reduced - Optimizing parameters... improved 0.015 lnL - Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16666,79 +16663,76 @@ Subset 3: Random seed for bootstrap reweighting: 486988955 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1593, seed 1137050303, best lnL -13370.482 +Bootstrap rep 1 (of 1) generation 1094, seed 1931684846, best lnL -13370.587 gen current_lnL precision last_tree_imp -1593 -13370.4816 0.206 0 -1600 -13370.4816 0.206 0 -1700 -13370.4688 0.206 0 -1800 -13370.4569 0.206 0 -1900 -13370.4339 0.206 0 -2000 -13370.4174 0.206 0 -Optimization precision reduced - Optimizing parameters... improved 0.006 lnL - Optimizing branchlengths... improved 0.000 lnL -NOTE: ****Specified generation limit (2000) reached... +1094 -13370.5873 0.304 0 +1100 -13370.5869 0.304 0 +1200 -13370.5241 0.304 0 +1300 -13370.5103 0.304 0 +1400 -13370.5063 0.304 0 +NOTE: ****Specified time limit (1 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: User specified matrix type: ( 0 1 2 2 3 4 ) - AC = 1.663, AG = 2.558, AT = 1.235, CG = 1.235, CT = 4.221, GT = 1.000 + AC = 1.598, AG = 2.495, AT = 1.208, CG = 1.208, CT = 4.135, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3082 0.1810 0.3087 0.2020 + (ACGT) 0.3079 0.1814 0.3083 0.2024 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.3662 + 0.3640 Substitution rate categories under this model: rate proportion - 0.0122 0.2500 - 0.1561 0.2500 - 0.6919 0.2500 - 3.1398 0.2500 + 0.0119 0.2500 + 0.1544 0.2500 + 0.6892 0.2500 + 3.1446 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 = 2.621, AG = 4.245, AT = 0.820, CG = 4.245, CT = 2.621, GT = 1.000 + AC = 2.627, AG = 4.239, AT = 0.821, CG = 4.239, CT = 2.627, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2814 0.1768 0.1593 0.3825 + (ACGT) 0.2812 0.1772 0.1597 0.3819 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 0.2457 + 0.2460 Substitution rate categories under this model: rate proportion 0.0019 0.2500 - 0.0636 0.2500 - 0.4923 0.2500 - 3.4422 0.2500 + 0.0638 0.2500 + 0.4929 0.2500 + 3.4413 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 = 5.311, AT = 4.291, CG = 0.629, CT = 5.311, GT = 1.000 + AC = 1.000, AG = 5.333, AT = 4.290, CG = 0.632, CT = 5.333, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1554 0.3464 0.2763 0.2219 + (ACGT) 0.1555 0.3460 0.2768 0.2217 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 4.1264 + 4.1101 with an invariant (invariable) site category, proportion estimated - 0.0487 + 0.0486 Substitution rate categories under this model: rate proportion - 0.0000 0.0487 - 0.4612 0.2378 - 0.7795 0.2378 - 1.0844 0.2378 - 1.6750 0.2378 + 0.0000 0.0486 + 0.4603 0.2379 + 0.7789 0.2379 + 1.0844 0.2379 + 1.6764 0.2379 Subset rate multipliers: 0.53 0.29 2.18 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) No branches were short enough to be 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!*** @@ -16748,25 +16742,25 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13370.4112 +Replicate 1 : -13370.4986 (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: 1.663 2.558 1.235 1.235 4.221 1 0.308 0.181 0.309 0.202 0.366 +rep 1: 1.598 2.495 1.208 1.208 4.135 1 0.308 0.181 0.308 0.202 0.364 Partition model subset 2: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha -rep 1: 2.621 4.245 0.8204 4.245 2.621 1 0.281 0.177 0.159 0.382 0.246 +rep 1: 2.627 4.239 0.8212 4.239 2.627 1 0.281 0.177 0.160 0.382 0.246 Partition model subset 3: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 1 5.311 4.291 0.6292 5.311 1 0.155 0.346 0.276 0.222 4.126 0.049 +rep 1: 1 5.333 4.29 0.6325 5.333 1 0.155 0.346 0.277 0.222 4.110 0.049 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 1.762 0.530 0.287 2.183 +rep 1: 1.764 0.530 0.287 2.183 Saving best tree to bootstrap file ch.p.3diff.boot.tre @@ -17089,7 +17083,6 @@ 2300 -467.7087 0.010 0 2400 -467.7083 0.010 0 2500 -467.7076 0.010 0 -2600 -467.7072 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -17215,9 +17208,10 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2675, seed 408757040, best lnL -467.707 +Search rep 2 (of 5) generation 2584, seed 1571419875, best lnL -467.707 gen current_lnL precision last_tree_imp -2675 -467.7072 0.010 0 +2584 -467.7072 0.010 0 +2600 -467.7072 0.010 0 2700 -467.7072 0.010 0 2800 -467.7067 0.010 0 2900 -467.7065 0.010 0 @@ -17258,7 +17252,7 @@ pass 14: -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 7 seconds +Time used so far = 0 hours, 0 minutes and 8 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17361,153 +17355,29 @@ 2500 -467.7194 0.010 0 2600 -467.7186 0.010 0 2700 -467.7173 0.010 0 -2800 -467.7170 0.010 0 -2900 -467.7164 0.010 0 -3000 -467.7153 0.010 0 -3100 -467.7148 0.010 0 -3200 -467.7140 0.010 0 -3300 -467.7139 0.010 0 -3400 -467.7136 0.010 0 -3500 -467.7136 0.010 0 -3600 -467.7132 0.010 0 -3700 -467.7130 0.010 0 -3800 -467.7129 0.010 0 -3900 -467.7124 0.010 0 -4000 -467.7117 0.010 0 -4100 -467.7113 0.010 0 -4200 -467.7110 0.010 0 -4300 -467.7107 0.010 0 -4400 -467.7102 0.010 0 -4500 -467.7101 0.010 0 -4600 -467.7097 0.010 0 -4700 -467.7090 0.010 0 -4800 -467.7087 0.010 0 -4900 -467.7086 0.010 0 -5000 -467.7086 0.010 0 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -467.7085 0.010 0 -5200 -467.7083 0.010 0 -Reached termination condition! -last topological improvement at gen 0 -Improvement over last 500 gen = 0.00073 -Current score = -467.7083 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -467.7172 Performing final optimizations... -pass 1 : -467.7083 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -467.6995 (branch= 0.0088 subset rates= 0.0000) -pass 3 : -467.6892 (branch= 0.0102 subset rates= 0.0000) -pass 4 : -467.6873 (branch= 0.0018 subset rates= 0.0001) -pass 5 : -467.6835 (branch= 0.0038 subset rates= 0.0000) -pass 6 : -467.6812 (branch= 0.0024 subset rates= 0.0000) -pass 7 : -467.6800 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -467.6794 (branch= 0.0006 subset rates= 0.0000) -pass 9 : -467.6788 (branch= 0.0004 subset rates= 0.0002) -pass 10: -467.6785 (branch= 0.0003 subset rates= 0.0000) -pass 11: -467.6783 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6782 (branch= 0.0001 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 1 : -467.7172 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.7019 (branch= 0.0152 subset rates= 0.0000) +pass 3 : -467.6945 (branch= 0.0074 subset rates= 0.0000) +pass 4 : -467.6915 (branch= 0.0030 subset rates= 0.0000) +pass 5 : -467.6869 (branch= 0.0046 subset rates= 0.0000) +pass 6 : -467.6831 (branch= 0.0036 subset rates= 0.0003) +pass 7 : -467.6810 (branch= 0.0021 subset rates= 0.0000) +pass 8 : -467.6796 (branch= 0.0014 subset rates= 0.0000) +pass 9 : -467.6790 (branch= 0.0006 subset rates= 0.0000) +pass 10: -467.6787 (branch= 0.0003 subset rates= 0.0000) +pass 11: -467.6786 (branch= 0.0001 subset rates= 0.0000) +pass 12: -467.6785 (branch= 0.0001 subset rates= 0.0001) +pass 13: -467.6783 (branch= 0.0002 subset rates= 0.0000) +pass 14: -467.6782 (branch= 0.0001 subset rates= 0.0000) pass 15: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 16: -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 12 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 2.19 -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=197530422 - -Initial ln Likelihood: -623.7387 -optimizing: starting branch lengths, subset rates... -pass 1:+ 137.787 (branch= 132.34 scale= 1.23 subset rates= 4.21) -pass 2:+ 11.487 (branch= 10.58 scale= 0.00 subset rates= 0.91) -pass 3:+ 3.956 (branch= 3.81 scale= 0.00 subset rates= 0.15) -pass 4:+ 2.524 (branch= 2.47 scale= 0.03 subset rates= 0.02) -pass 5:+ 0.096 (branch= 0.10 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.010 (branch= 0.01 scale= 0.00 subset rates= 0.00) -lnL after optimization: -467.8781 -gen current_lnL precision last_tree_imp -0 -467.8781 0.010 0 -NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.8781 -Performing final optimizations... -pass 1 : -467.8283 (branch= 0.0468 subset rates= 0.0030) -pass 2 : -467.7219 (branch= 0.1063 subset rates= 0.0002) -pass 3 : -467.6989 (branch= 0.0229 subset rates= 0.0000) -pass 4 : -467.6884 (branch= 0.0104 subset rates= 0.0001) -pass 5 : -467.6834 (branch= 0.0050 subset rates= 0.0000) -pass 6 : -467.6818 (branch= 0.0016 subset rates= 0.0000) -pass 7 : -467.6800 (branch= 0.0017 subset rates= 0.0000) -pass 8 : -467.6792 (branch= 0.0005 subset rates= 0.0004) -pass 9 : -467.6787 (branch= 0.0005 subset rates= 0.0000) -pass 10: -467.6785 (branch= 0.0002 subset rates= 0.0000) -pass 11: -467.6784 (branch= 0.0001 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0001 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) -pass 15: -467.6783 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -467.6783 -Time used so far = 0 hours, 0 minutes and 12 seconds - MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 2 (standard data) @@ -17538,7 +17408,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 4 (of 5)<<< +>>>Terminated Search rep 3 (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!*** @@ -17546,15 +17416,14 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 3 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 : -467.6797 Replicate 2 : -467.6782 (same topology as 1) -Replicate 3 : -467.6782 (best) (same topology as 1) -Replicate 4 : -467.6783 (same topology as 1) (TERMINATED PREMATURELY) +Replicate 3 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -17571,8 +17440,7 @@ TL R(1) R(2) R(3) rep 1: 3.838 0.789 1.477 2.150 rep 2: 3.842 0.786 1.478 2.181 -rep 3: 3.844 0.786 1.480 2.187 -rep 4: 3.844 0.785 1.481 2.188 +rep 3: 3.844 0.786 1.477 2.190 Saving final tree from best search rep (#3) to ch.p.mk.ssr.best.tre ####################################################### @@ -17789,7 +17657,7 @@ pass 14: -477.2120 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2120 -Time used so far = 0 hours, 0 minutes and 2 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -17871,38 +17739,6 @@ 300 -477.7353 0.010 130 400 -477.7275 0.010 130 500 -477.6996 0.010 130 -600 -477.6937 0.010 130 -700 -477.6851 0.010 130 -800 -477.6799 0.010 130 -900 -477.6767 0.010 130 -1000 -477.6710 0.010 130 -1100 -477.6699 0.010 130 -1200 -477.6686 0.010 130 -1300 -477.6638 0.010 130 -1400 -477.6624 0.010 130 -1500 -477.6619 0.010 130 -1600 -477.6612 0.010 130 -1700 -477.6603 0.010 130 -1800 -477.6599 0.010 130 -1900 -477.4948 0.010 1880 -2000 -477.4872 0.010 1880 -2100 -477.4843 0.010 1880 -2200 -477.4818 0.010 1880 -2300 -477.4783 0.010 1880 -2400 -477.4777 0.010 1880 -2500 -477.4765 0.010 1880 -2600 -477.4764 0.010 1880 -2700 -477.4764 0.010 1880 -2800 -477.4727 0.010 1880 -2900 -477.4717 0.010 1880 -3000 -477.4708 0.010 1880 -3100 -477.4705 0.010 1880 -3200 -477.4695 0.010 1880 -3300 -477.4684 0.010 1880 -3400 -477.4676 0.010 1880 -3500 -477.4676 0.010 1880 -3600 -477.4670 0.010 1880 -3700 -477.4656 0.010 1880 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18028,9 +17864,41 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 3751, seed 1841286613, best lnL -477.465 +Search rep 2 (of 5) generation 581, seed 947048988, best lnL -477.694 gen current_lnL precision last_tree_imp -3751 -477.4654 0.010 1880 +581 -477.6937 0.010 130 +600 -477.6937 0.010 130 +700 -477.6851 0.010 130 +800 -477.6799 0.010 130 +900 -477.6767 0.010 130 +1000 -477.6710 0.010 130 +1100 -477.6699 0.010 130 +1200 -477.6686 0.010 130 +1300 -477.6638 0.010 130 +1400 -477.6624 0.010 130 +1500 -477.6619 0.010 130 +1600 -477.6612 0.010 130 +1700 -477.6603 0.010 130 +1800 -477.6599 0.010 130 +1900 -477.4948 0.010 1880 +2000 -477.4872 0.010 1880 +2100 -477.4843 0.010 1880 +2200 -477.4818 0.010 1880 +2300 -477.4783 0.010 1880 +2400 -477.4777 0.010 1880 +2500 -477.4765 0.010 1880 +2600 -477.4764 0.010 1880 +2700 -477.4764 0.010 1880 +2800 -477.4727 0.010 1880 +2900 -477.4717 0.010 1880 +3000 -477.4708 0.010 1880 +3100 -477.4705 0.010 1880 +3200 -477.4695 0.010 1880 +3300 -477.4684 0.010 1880 +3400 -477.4676 0.010 1880 +3500 -477.4676 0.010 1880 +3600 -477.4670 0.010 1880 +3700 -477.4656 0.010 1880 3800 -477.4653 0.010 1880 3900 -477.4647 0.010 1880 4000 -477.4645 0.010 1880 @@ -18047,182 +17915,26 @@ Optimizing parameters... improved 0.000 lnL Optimizing branchlengths... improved 0.000 lnL 5100 -477.4588 0.010 1880 -5200 -477.4582 0.010 1880 -5300 -477.4576 0.010 1880 -5400 -477.4575 0.010 1880 -5500 -477.4573 0.010 1880 -5600 -477.4573 0.010 1880 -5700 -477.4564 0.010 1880 -5800 -477.4564 0.010 1880 -5900 -477.4564 0.010 1880 -6000 -477.4560 0.010 1880 -6100 -477.4560 0.010 1880 -6200 -477.4560 0.010 1880 -Reached termination condition! -last topological improvement at gen 1880 -Improvement over last 500 gen = 0.00042 -Current score = -477.4560 -Performing final optimizations... -pass 1 : -477.4560 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4438 (branch= 0.0122 subset rates= 0.0000) -pass 3 : -477.4415 (branch= 0.0023 subset rates= 0.0000) -pass 4 : -477.4374 (branch= 0.0033 subset rates= 0.0007) -pass 5 : -477.4358 (branch= 0.0017 subset rates= 0.0000) -pass 6 : -477.4336 (branch= 0.0021 subset rates= 0.0000) -pass 7 : -477.4335 (branch= 0.0001 subset rates= 0.0000) -pass 8 : -477.4332 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -477.4326 (branch= 0.0005 subset rates= 0.0000) -pass 10: -477.4324 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4323 (branch= 0.0001 subset rates= 0.0000) -pass 12: -477.4322 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4322 (branch= 0.0000 subset rates= 0.0000) -pass 14: -477.4317 (branch= 0.0000 subset rates= 0.0005) -pass 15: -477.4316 (branch= 0.0001 subset rates= 0.0000) -pass 16: -477.4316 (branch= 0.0000 subset rates= 0.0000) -pass 17: -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 8 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 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 (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=453275776 - -Initial ln Likelihood: -655.4069 -optimizing: starting branch lengths, subset rates... -pass 1:+ 162.712 (branch= 151.74 scale= 0.80 subset rates= 10.17) -pass 2:+ 11.123 (branch= 7.12 scale= 0.00 subset rates= 4.00) -pass 3:+ 2.644 (branch= 1.41 scale= 0.02 subset rates= 1.22) -pass 4:+ 0.914 (branch= 0.60 scale= 0.02 subset rates= 0.29) -pass 5:+ 0.151 (branch= 0.14 scale= 0.00 subset rates= 0.01) -pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -477.8619 -gen current_lnL precision last_tree_imp -0 -477.8619 0.010 0 -100 -477.7580 0.010 69 -200 -477.7356 0.010 69 -300 -477.5717 0.010 267 -400 -477.5393 0.010 267 -500 -477.5344 0.010 267 -600 -477.5233 0.010 267 -700 -477.5160 0.010 267 -800 -477.5080 0.010 267 -900 -477.5030 0.010 267 -1000 -477.4960 0.010 267 -1100 -477.4913 0.010 267 -1200 -477.4892 0.010 267 -1300 -477.4883 0.010 267 -1400 -477.4865 0.010 267 -1500 -477.4865 0.010 267 -1600 -477.4854 0.010 267 -1700 -477.4847 0.010 267 -1800 -477.4835 0.010 267 -1900 -477.4824 0.010 267 -2000 -477.4818 0.010 267 -2100 -477.4797 0.010 267 -2200 -477.4761 0.010 267 -2300 -477.4739 0.010 267 -2400 -477.4729 0.010 267 -2500 -477.4710 0.010 267 -2600 -477.4696 0.010 267 -2700 -477.4691 0.010 267 -2800 -477.4686 0.010 267 -2900 -477.4677 0.010 267 -3000 -477.4670 0.010 267 -3100 -477.4665 0.010 267 -3200 -477.4664 0.010 267 -3300 -477.4662 0.010 267 -3400 -477.4659 0.010 267 -3500 -477.4655 0.010 267 -3600 -477.4644 0.010 267 -3700 -477.4643 0.010 267 -3800 -477.4641 0.010 267 -3900 -477.4633 0.010 267 -4000 -477.4629 0.010 267 -4100 -477.4623 0.010 267 -4200 -477.4619 0.010 267 -4300 -477.4607 0.010 267 -4400 -477.4607 0.010 267 -4500 -477.4607 0.010 267 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.4607 +Current score = -477.4584 Performing final optimizations... -pass 1 : -477.4607 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -477.4482 (branch= 0.0125 subset rates= 0.0000) -pass 3 : -477.4396 (branch= 0.0086 subset rates= 0.0000) -pass 4 : -477.4382 (branch= 0.0014 subset rates= 0.0000) -pass 5 : -477.4363 (branch= 0.0019 subset rates= 0.0000) -pass 6 : -477.4345 (branch= 0.0018 subset rates= 0.0000) -pass 7 : -477.4333 (branch= 0.0013 subset rates= 0.0000) -pass 8 : -477.4328 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -477.4325 (branch= 0.0003 subset rates= 0.0000) -pass 10: -477.4323 (branch= 0.0002 subset rates= 0.0000) -pass 11: -477.4318 (branch= 0.0001 subset rates= 0.0003) -pass 12: -477.4317 (branch= 0.0001 subset rates= 0.0000) -pass 13: -477.4316 (branch= 0.0001 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 : -477.4584 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -477.4434 (branch= 0.0147 subset rates= 0.0002) +pass 3 : -477.4382 (branch= 0.0038 subset rates= 0.0015) +pass 4 : -477.4363 (branch= 0.0019 subset rates= 0.0001) +pass 5 : -477.4351 (branch= 0.0011 subset rates= 0.0000) +pass 6 : -477.4334 (branch= 0.0017 subset rates= 0.0000) +pass 7 : -477.4327 (branch= 0.0007 subset rates= 0.0000) +pass 8 : -477.4324 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -477.4321 (branch= 0.0003 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: -477.4318 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.4318 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.4318 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.4318 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -477.4316 +Final score = -477.4317 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18255,7 +17967,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 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!*** @@ -18263,14 +17975,13 @@ ####################################################### -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 : -477.2120 (best) -Replicate 2 : -477.4316 -Replicate 3 : -477.4316 (same topology as 2) (TERMINATED PREMATURELY) +Replicate 2 : -477.4317 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -18286,8 +17997,7 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.671 0.643 1.905 2.626 -rep 2: 4.930 0.631 1.915 2.743 -rep 3: 4.927 0.632 1.912 2.739 +rep 2: 4.926 0.633 1.909 2.741 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -18513,7 +18223,7 @@ pass 12: -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 3 seconds +Time used so far = 0 hours, 0 minutes and 5 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18575,32 +18285,6 @@ 300 -427.6003 0.010 249 400 -427.5649 0.010 249 500 -427.4911 0.010 499 -600 -427.3864 0.010 511 -700 -425.7188 0.010 668 -800 -425.6951 0.010 722 -900 -425.6795 0.010 722 -1000 -425.6689 0.010 722 -1100 -425.6640 0.010 722 -1200 -425.6430 0.010 722 -1300 -425.6381 0.010 722 -1400 -425.6345 0.010 722 -1500 -425.6341 0.010 722 -1600 -425.6274 0.010 722 -1700 -425.6239 0.010 722 -1800 -425.6235 0.010 722 -1900 -425.6225 0.010 722 -2000 -425.6202 0.010 722 -2100 -425.6196 0.010 722 -2200 -425.6174 0.010 722 -2300 -425.6146 0.010 722 -2400 -425.6135 0.010 722 -2500 -425.6104 0.010 722 -2600 -425.6099 0.010 722 -2700 -425.6088 0.010 722 -2800 -425.6077 0.010 722 -2900 -425.6073 0.010 722 -3000 -425.6058 0.010 722 -3100 -425.6056 0.010 722 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -18729,9 +18413,35 @@ Subset 3: Random seed for bootstrap reweighting: 974568031 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 3177, seed 1759019936, best lnL -425.606 +Bootstrap rep 1 (of 1) Search rep 2 (of 5) generation 563, seed 583506664, best lnL -427.391 gen current_lnL precision last_tree_imp -3177 -425.6055 0.010 722 +563 -427.3906 0.010 511 +600 -427.3864 0.010 511 +700 -425.7188 0.010 668 +800 -425.6951 0.010 722 +900 -425.6795 0.010 722 +1000 -425.6689 0.010 722 +1100 -425.6640 0.010 722 +1200 -425.6430 0.010 722 +1300 -425.6381 0.010 722 +1400 -425.6345 0.010 722 +1500 -425.6341 0.010 722 +1600 -425.6274 0.010 722 +1700 -425.6239 0.010 722 +1800 -425.6235 0.010 722 +1900 -425.6225 0.010 722 +2000 -425.6202 0.010 722 +2100 -425.6196 0.010 722 +2200 -425.6174 0.010 722 +2300 -425.6146 0.010 722 +2400 -425.6135 0.010 722 +2500 -425.6104 0.010 722 +2600 -425.6099 0.010 722 +2700 -425.6088 0.010 722 +2800 -425.6077 0.010 722 +2900 -425.6073 0.010 722 +3000 -425.6058 0.010 722 +3100 -425.6056 0.010 722 3200 -425.6055 0.010 722 3300 -425.6051 0.010 722 3400 -425.6049 0.010 722 @@ -18757,7 +18467,7 @@ pass 13: -425.5492 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.5492 -Time used so far = 0 hours, 0 minutes and 6 seconds +Time used so far = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -18821,145 +18531,24 @@ 1400 -425.3887 0.010 803 1500 -425.3865 0.010 803 1600 -425.3820 0.010 803 -1700 -425.3760 0.010 803 -1800 -425.3759 0.010 803 -1900 -425.3750 0.010 803 -2000 -425.3712 0.010 803 -2100 -425.3702 0.010 803 -2200 -425.3666 0.010 803 -2300 -425.3654 0.010 803 -2400 -425.3635 0.010 803 -2500 -425.3630 0.010 803 -2600 -425.3623 0.010 803 -2700 -425.3620 0.010 803 -2800 -425.3614 0.010 803 -2900 -425.3593 0.010 803 -3000 -425.3584 0.010 803 -3100 -425.3582 0.010 803 -3200 -425.3573 0.010 803 -3300 -425.3569 0.010 803 -3400 -425.3569 0.010 803 -3500 -425.3566 0.010 803 -3600 -425.3560 0.010 803 -3700 -425.3555 0.010 803 -3800 -425.3551 0.010 803 -3900 -425.3542 0.010 803 -4000 -425.3542 0.010 803 -4100 -425.3538 0.010 803 -4200 -425.3536 0.010 803 -4300 -425.3535 0.010 803 -4400 -425.3534 0.010 803 -Reached termination condition! -last topological improvement at gen 803 -Improvement over last 500 gen = 0.00083 -Current score = -425.3534 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -425.3768 Performing final optimizations... -pass 1 : -425.3485 (branch= 0.0000 subset rates= 0.0049) -pass 2 : -425.3321 (branch= 0.0164 subset rates= 0.0000) -pass 3 : -425.3250 (branch= 0.0071 subset rates= 0.0000) -pass 4 : -425.3223 (branch= 0.0027 subset rates= 0.0000) -pass 5 : -425.3220 (branch= 0.0003 subset rates= 0.0000) -pass 6 : -425.3220 (branch= 0.0000 subset rates= 0.0000) -pass 7 : -425.3215 (branch= 0.0005 subset rates= 0.0000) -pass 8 : -425.3208 (branch= 0.0007 subset rates= 0.0000) -pass 9 : -425.3207 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.3206 (branch= 0.0001 subset rates= 0.0000) -pass 11: -425.3206 (branch= 0.0000 subset rates= 0.0000) -pass 12: -425.3206 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -425.3744 (branch= 0.0000 subset rates= 0.0023) +pass 2 : -425.3424 (branch= 0.0300 subset rates= 0.0020) +pass 3 : -425.3313 (branch= 0.0097 subset rates= 0.0013) +pass 4 : -425.3262 (branch= 0.0052 subset rates= 0.0000) +pass 5 : -425.3237 (branch= 0.0025 subset rates= 0.0000) +pass 6 : -425.3218 (branch= 0.0019 subset rates= 0.0000) +pass 7 : -425.3210 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -425.3207 (branch= 0.0003 subset rates= 0.0000) +pass 9 : -425.3206 (branch= 0.0001 subset rates= 0.0000) +pass 10: -425.3205 (branch= 0.0000 subset rates= 0.0000) +pass 11: -425.3205 (branch= 0.0000 subset rates= 0.0000) +pass 12: -425.3205 (branch= 0.0000 subset rates= 0.0000) pass 13: -425.3205 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -425.3205 -Time used so far = 0 hours, 0 minutes and 10 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: - 0.86 1.55 1.15 -NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 9 branches were collapsed. - ->>>Completed Bootstrap rep 1 (of 1) Search rep 3 (of 5)<<< - ->>>Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< -Obtained starting tree 1 from Nexus -Starting with seed=1573911897 - -Initial ln Likelihood: -585.3657 -optimizing: starting branch lengths, subset rates... -pass 1:+ 128.924 (branch= 128.21 scale= 0.69 subset rates= 0.02) -pass 2:+ 11.959 (branch= 11.78 scale= 0.03 subset rates= 0.15) -pass 3:+ 4.421 (branch= 4.33 scale= 0.00 subset rates= 0.09) -pass 4:+ 0.779 (branch= 0.76 scale= 0.00 subset rates= 0.01) -pass 5:+ 0.057 (branch= 0.06 scale= 0.00 subset rates= 0.00) -pass 6:+ 0.012 (branch= 0.01 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -439.2135 -gen current_lnL precision last_tree_imp -0 -439.2135 0.010 0 -100 -428.1779 0.010 67 -200 -427.4638 0.010 189 -300 -427.4437 0.010 226 -400 -427.1435 0.010 393 -500 -427.1285 0.010 393 -600 -427.1120 0.010 393 -700 -427.1022 0.010 393 -800 -427.1003 0.010 393 -900 -427.0977 0.010 393 -1000 -427.0972 0.010 393 -1100 -427.0948 0.010 393 -1200 -427.0919 0.010 393 -1300 -427.0909 0.010 393 -1400 -427.0892 0.010 393 -1500 -427.0880 0.010 393 -1600 -427.0868 0.010 393 -1700 -427.0861 0.010 393 -1800 -427.0846 0.010 393 -1900 -425.5433 0.010 1890 -2000 -425.5081 0.010 1942 -2100 -425.3789 0.010 2010 -2200 -425.3685 0.010 2010 -2300 -425.3666 0.010 2010 -NOTE: ****Specified time limit (5 seconds) reached... -Current score = -425.3666 -Performing final optimizations... -pass 1 : -425.3666 (branch= 0.0000 subset rates= 0.0000) -pass 2 : -425.3329 (branch= 0.0336 subset rates= 0.0001) -pass 3 : -425.3299 (branch= 0.0030 subset rates= 0.0000) -pass 4 : -425.3268 (branch= 0.0031 subset rates= 0.0000) -pass 5 : -425.3226 (branch= 0.0042 subset rates= 0.0000) -pass 6 : -425.3212 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -425.3209 (branch= 0.0003 subset rates= 0.0000) -pass 8 : -425.3206 (branch= 0.0003 subset rates= 0.0000) -pass 9 : -425.3205 (branch= 0.0001 subset rates= 0.0000) -pass 10: -425.3204 (branch= 0.0001 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) -Looking for minimum length branches... -Final score = -425.3204 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -18988,11 +18577,11 @@ no rate heterogeneity Subset rate multipliers: - 0.86 1.54 1.14 + 0.87 1.53 1.14 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 10 branches were collapsed. + 9 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 4 (of 5)<<< +>>>Terminated Bootstrap rep 1 (of 1) Search rep 3 (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!*** @@ -19000,15 +18589,14 @@ ####################################################### -Completed 4 replicate search(es) (of 5). +Completed 3 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 : -425.5492 -Replicate 3 : -425.3205 -Replicate 4 : -425.3204 (best) (TERMINATED PREMATURELY) +Replicate 3 : -425.3205 (best) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19025,10 +18613,9 @@ TL R(1) R(2) R(3) rep 1: 3.038 0.868 1.530 1.121 rep 2: 3.039 0.868 1.535 1.108 -rep 3: 2.976 0.862 1.548 1.149 -rep 4: 2.982 0.865 1.539 1.142 +rep 3: 2.981 0.866 1.532 1.145 -Saving tree from best search rep (#4) to bootstrap file ch.p.mkv.ssr.boot.tre +Saving tree from best search rep (#3) to bootstrap file ch.p.mkv.ssr.boot.tre WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### @@ -19225,131 +18812,6 @@ 2900 -473.9777 0.010 653 3000 -473.9769 0.010 653 3100 -473.9769 0.010 653 -3200 -473.9768 0.010 653 -3300 -473.9767 0.010 653 -3400 -473.9765 0.010 653 -3500 -473.9764 0.010 653 -Reached termination condition! -last topological improvement at gen 653 -Improvement over last 500 gen = 0.00052 -Current score = -473.9764 -Performing final optimizations... -pass 1 : -473.9751 (branch= 0.0001 subset rates= 0.0013) -pass 2 : -473.9549 (branch= 0.0185 subset rates= 0.0017) -pass 3 : -473.9549 (branch= 0.0000 subset rates= 0.0000) -pass 4 : -473.9549 (branch= 0.0000 subset rates= 0.0000) -pass 5 : -473.9531 (branch= 0.0017 subset rates= 0.0000) -pass 6 : -473.9528 (branch= 0.0004 subset rates= 0.0000) -pass 7 : -473.9522 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9517 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -473.9514 (branch= 0.0003 subset rates= 0.0000) -pass 10: -473.9514 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9513 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9513 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9513 (branch= 0.0000 subset rates= 0.0000) -pass 14: -473.9513 (branch= 0.0000 subset rates= 0.0000) -Looking for minimum length branches... -Final score = -473.9513 -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 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 2.06 2.83 -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=966839612 - -Initial ln Likelihood: -700.9766 -optimizing: starting branch lengths, subset rates... -pass 1:+ 200.092 (branch= 188.08 scale= 2.23 subset rates= 9.79) -pass 2:+ 16.922 (branch= 12.34 scale= 0.03 subset rates= 4.55) -pass 3:+ 7.545 (branch= 5.75 scale= 0.00 subset rates= 1.79) -pass 4:+ 1.489 (branch= 0.84 scale= 0.00 subset rates= 0.65) -pass 5:+ 0.089 (branch= 0.04 scale= 0.01 subset rates= 0.04) -pass 6:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) -pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8241 -gen current_lnL precision last_tree_imp -0 -474.8241 0.010 0 -100 -474.8003 0.010 0 -200 -474.7018 0.010 199 -300 -474.6989 0.010 199 -400 -474.6893 0.010 199 -500 -474.5615 0.010 476 -600 -474.5539 0.010 476 -700 -474.5465 0.010 476 -800 -474.5376 0.010 476 -900 -474.5300 0.010 476 -1000 -474.5272 0.010 476 -1100 -474.5251 0.010 476 -1200 -474.5238 0.010 476 -1300 -474.5141 0.010 476 -1400 -474.5121 0.010 476 -1500 -474.5085 0.010 476 -1600 -474.5066 0.010 476 -1700 -474.5062 0.010 476 -1800 -474.5050 0.010 476 -1900 -474.5037 0.010 476 -2000 -474.5012 0.010 476 -2100 -474.5010 0.010 476 -2200 -474.5000 0.010 476 -2300 -474.4991 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -19475,77 +18937,35 @@ STARTING RUN Restarting from checkpoint... -Search rep 2 (of 5) generation 2309, seed 742234913, best lnL -474.499 +Search rep 1 (of 5) generation 3148, seed 1258364851, best lnL -473.977 gen current_lnL precision last_tree_imp -2309 -474.4991 0.010 476 -2400 -474.4949 0.010 476 -2500 -474.4943 0.010 476 -2600 -474.4909 0.010 476 -2700 -474.4903 0.010 476 -2800 -474.4894 0.010 476 -2900 -474.4883 0.010 476 -3000 -474.4861 0.010 476 -3100 -474.4850 0.010 476 -3200 -474.4849 0.010 476 -3300 -474.4829 0.010 476 -3400 -474.4819 0.010 476 -3500 -474.4807 0.010 476 -3600 -474.4802 0.010 476 -3700 -474.4800 0.010 476 -3800 -474.4793 0.010 476 -3900 -474.4778 0.010 476 -4000 -474.4776 0.010 476 -4100 -474.4776 0.010 476 -4200 -474.4762 0.010 476 -4300 -474.4756 0.010 476 -4400 -474.4744 0.010 476 -4500 -474.4737 0.010 476 -4600 -474.4714 0.010 476 -4700 -474.4703 0.010 476 -4800 -474.4690 0.010 476 -4900 -474.4690 0.010 476 -5000 -474.4685 0.010 476 - Optimizing parameters... improved 0.000 lnL - Optimizing branchlengths... improved 0.000 lnL -5100 -474.4614 0.010 476 -5200 -474.4602 0.010 476 -5300 -474.4597 0.010 476 -5400 -474.4595 0.010 476 -5500 -474.4591 0.010 476 -5600 -474.4574 0.010 476 -5700 -474.4571 0.010 476 -5800 -474.4562 0.010 476 -5900 -474.4562 0.010 476 -6000 -474.4553 0.010 476 -6100 -474.4552 0.010 476 -6200 -474.4552 0.010 476 -6300 -474.4552 0.010 476 +3148 -473.9769 0.010 653 +3200 -473.9768 0.010 653 +3300 -473.9767 0.010 653 +3400 -473.9765 0.010 653 +3500 -473.9764 0.010 653 Reached termination condition! -last topological improvement at gen 476 -Improvement over last 500 gen = 0.00100 -Current score = -474.4552 +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00052 +Current score = -473.9764 Performing final optimizations... -pass 1 : -474.4503 (branch= 0.0049 subset rates= 0.0000) -pass 2 : -474.4381 (branch= 0.0122 subset rates= 0.0000) -pass 3 : -474.4341 (branch= 0.0040 subset rates= 0.0000) -pass 4 : -474.4333 (branch= 0.0008 subset rates= 0.0000) -pass 5 : -474.4329 (branch= 0.0004 subset rates= 0.0000) -pass 6 : -474.4315 (branch= 0.0014 subset rates= 0.0000) -pass 7 : -474.4304 (branch= 0.0011 subset rates= 0.0000) -pass 8 : -474.4298 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -474.4295 (branch= 0.0004 subset rates= 0.0000) -pass 10: -474.4293 (branch= 0.0002 subset rates= 0.0000) -pass 11: -474.4285 (branch= 0.0001 subset rates= 0.0007) -pass 12: -474.4283 (branch= 0.0002 subset rates= 0.0000) -pass 13: -474.4283 (branch= 0.0001 subset rates= 0.0000) -pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 15: -474.4282 (branch= 0.0000 subset rates= 0.0000) -pass 16: -474.4281 (branch= 0.0000 subset rates= 0.0000) -pass 17: -474.4281 (branch= 0.0000 subset rates= 0.0000) -pass 18: -474.4281 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -473.9751 (branch= 0.0001 subset rates= 0.0013) +pass 2 : -473.9549 (branch= 0.0185 subset rates= 0.0017) +pass 3 : -473.9549 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9549 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -473.9531 (branch= 0.0017 subset rates= 0.0000) +pass 6 : -473.9528 (branch= 0.0004 subset rates= 0.0000) +pass 7 : -473.9522 (branch= 0.0006 subset rates= 0.0000) +pass 8 : -473.9517 (branch= 0.0005 subset rates= 0.0000) +pass 9 : -473.9514 (branch= 0.0003 subset rates= 0.0000) +pass 10: -473.9514 (branch= 0.0001 subset rates= 0.0000) +pass 11: -473.9513 (branch= 0.0000 subset rates= 0.0000) +pass 12: -473.9513 (branch= 0.0000 subset rates= 0.0000) +pass 13: -473.9513 (branch= 0.0000 subset rates= 0.0000) +pass 14: -473.9513 (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 9 seconds +Final score = -473.9513 +Time used so far = 0 hours, 0 minutes and 6 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -19573,13 +18993,13 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.03 2.92 + 0.59 2.06 2.83 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 7 branches were collapsed. + 8 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 @@ -19608,61 +19028,82 @@ Subset rate multipliers: 1.00 1.00 1.00 -Starting with seed=2147279092 +Starting with seed=966839612 -Initial ln Likelihood: -670.9670 +Initial ln Likelihood: -700.9766 optimizing: starting branch lengths, subset rates... -pass 1:+ 179.422 (branch= 168.15 scale= 0.61 subset rates= 10.66) -pass 2:+ 11.191 (branch= 6.35 scale= 0.00 subset rates= 4.84) -pass 3:+ 4.303 (branch= 2.55 scale= 0.00 subset rates= 1.75) -pass 4:+ 0.935 (branch= 0.32 scale= 0.00 subset rates= 0.62) -pass 5:+ 0.266 (branch= 0.22 scale= 0.00 subset rates= 0.05) -pass 6:+ 0.014 (branch= 0.01 scale= 0.00 subset rates= 0.00) +pass 1:+ 200.092 (branch= 188.08 scale= 2.23 subset rates= 9.79) +pass 2:+ 16.922 (branch= 12.34 scale= 0.03 subset rates= 4.55) +pass 3:+ 7.545 (branch= 5.75 scale= 0.00 subset rates= 1.79) +pass 4:+ 1.489 (branch= 0.84 scale= 0.00 subset rates= 0.65) +pass 5:+ 0.089 (branch= 0.04 scale= 0.01 subset rates= 0.04) +pass 6:+ 0.015 (branch= 0.02 scale= 0.00 subset rates= 0.00) pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) -lnL after optimization: -474.8353 +lnL after optimization: -474.8241 gen current_lnL precision last_tree_imp -0 -474.8353 0.010 0 -100 -474.0723 0.010 91 -200 -474.0453 0.010 91 -300 -474.0377 0.010 91 -400 -474.0274 0.010 91 -500 -474.0193 0.010 91 -600 -474.0136 0.010 91 -700 -474.0105 0.010 91 -800 -474.0078 0.010 91 -900 -474.0055 0.010 91 -1000 -474.0053 0.010 91 -1100 -474.0046 0.010 91 -1200 -474.0040 0.010 91 -1300 -474.0022 0.010 91 -1400 -474.0005 0.010 91 -1500 -473.9999 0.010 91 -1600 -473.9991 0.010 91 -1700 -473.9988 0.010 91 -1800 -473.9944 0.010 91 -1900 -473.9940 0.010 91 -2000 -473.9937 0.010 91 -2100 -473.9907 0.010 91 +0 -474.8241 0.010 0 +100 -474.8003 0.010 0 +200 -474.7018 0.010 199 +300 -474.6989 0.010 199 +400 -474.6893 0.010 199 +500 -474.5615 0.010 476 +600 -474.5539 0.010 476 +700 -474.5465 0.010 476 +800 -474.5376 0.010 476 +900 -474.5300 0.010 476 +1000 -474.5272 0.010 476 +1100 -474.5251 0.010 476 +1200 -474.5238 0.010 476 +1300 -474.5141 0.010 476 +1400 -474.5121 0.010 476 +1500 -474.5085 0.010 476 +1600 -474.5066 0.010 476 +1700 -474.5062 0.010 476 +1800 -474.5050 0.010 476 +1900 -474.5037 0.010 476 +2000 -474.5012 0.010 476 +2100 -474.5010 0.010 476 +2200 -474.5000 0.010 476 +2300 -474.4991 0.010 476 +2400 -474.4949 0.010 476 +2500 -474.4943 0.010 476 +2600 -474.4909 0.010 476 +2700 -474.4903 0.010 476 +2800 -474.4894 0.010 476 +2900 -474.4883 0.010 476 +3000 -474.4861 0.010 476 +3100 -474.4850 0.010 476 +3200 -474.4849 0.010 476 +3300 -474.4829 0.010 476 +3400 -474.4819 0.010 476 +3500 -474.4807 0.010 476 +3600 -474.4802 0.010 476 +3700 -474.4800 0.010 476 +3800 -474.4793 0.010 476 +3900 -474.4778 0.010 476 +4000 -474.4776 0.010 476 +4100 -474.4776 0.010 476 +4200 -474.4762 0.010 476 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9907 +Current score = -474.4756 Performing final optimizations... -pass 1 : -473.9861 (branch= 0.0000 subset rates= 0.0046) -pass 2 : -473.9655 (branch= 0.0188 subset rates= 0.0017) -pass 3 : -473.9612 (branch= 0.0043 subset rates= 0.0000) -pass 4 : -473.9570 (branch= 0.0042 subset rates= 0.0000) -pass 5 : -473.9543 (branch= 0.0027 subset rates= 0.0000) -pass 6 : -473.9533 (branch= 0.0011 subset rates= 0.0000) -pass 7 : -473.9529 (branch= 0.0004 subset rates= 0.0000) -pass 8 : -473.9521 (branch= 0.0008 subset rates= 0.0000) -pass 9 : -473.9519 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9519 (branch= 0.0000 subset rates= 0.0000) -pass 11: -473.9518 (branch= 0.0001 subset rates= 0.0000) -pass 12: -473.9518 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9508 (branch= 0.0000 subset rates= 0.0010) -pass 14: -473.9508 (branch= 0.0001 subset rates= 0.0000) -pass 15: -473.9508 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4693 (branch= 0.0063 subset rates= 0.0000) +pass 2 : -474.4562 (branch= 0.0125 subset rates= 0.0006) +pass 3 : -474.4453 (branch= 0.0109 subset rates= 0.0000) +pass 4 : -474.4374 (branch= 0.0079 subset rates= 0.0000) +pass 5 : -474.4341 (branch= 0.0033 subset rates= 0.0000) +pass 6 : -474.4318 (branch= 0.0023 subset rates= 0.0000) +pass 7 : -474.4302 (branch= 0.0015 subset rates= 0.0001) +pass 8 : -474.4295 (branch= 0.0007 subset rates= 0.0001) +pass 9 : -474.4288 (branch= 0.0007 subset rates= 0.0000) +pass 10: -474.4285 (branch= 0.0003 subset rates= 0.0000) +pass 11: -474.4283 (branch= 0.0002 subset rates= 0.0000) +pass 12: -474.4283 (branch= 0.0001 subset rates= 0.0000) +pass 13: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4282 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4282 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9508 +Final score = -474.4282 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -19691,11 +19132,11 @@ no rate heterogeneity Subset rate multipliers: - 0.59 2.07 2.81 + 0.59 2.03 2.93 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 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!*** @@ -19703,14 +19144,13 @@ ####################################################### -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 : -473.9513 -Replicate 2 : -474.4281 -Replicate 3 : -473.9508 (best) (same topology as 1) (TERMINATED PREMATURELY) +Replicate 1 : -473.9513 (best) +Replicate 2 : -474.4282 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -19726,10 +19166,9 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) rep 1: 4.351 0.588 2.060 2.828 -rep 2: 4.601 0.588 2.033 2.920 -rep 3: 4.350 0.588 2.065 2.810 +rep 2: 4.600 0.588 2.030 2.926 -Saving final tree from best search rep (#3) to ch.p.mkvO.ssr.best.tre +Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### TREEFILES PASS ALL TESTS COMPLETED SUCCESSFULLY @@ -19745,13 +19184,13 @@ create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - make -j16 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j15 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' @@ -19794,11 +19233,11 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-7_amd64.deb'. +dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-7_amd64.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-7_amd64.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-7_amd64.deb'. dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-7_amd64.deb'. -dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-7_all.deb'. dpkg-genbuildinfo --build=binary -O../garli_2.1-7_amd64.buildinfo dpkg-genchanges --build=binary -O../garli_2.1-7_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -19806,12 +19245,14 @@ 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/1501427/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1501427/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/3092069 and its subdirectories -I: Current time: Sun Jun 9 13:31:04 -12 2024 -I: pbuilder-time-stamp: 1717983064 +I: removing directory /srv/workspace/pbuilder/1501427 and its subdirectories +I: Current time: Tue May 9 09:19:38 +14 2023 +I: pbuilder-time-stamp: 1683573578