Diff of the two buildlogs: -- --- b1/build.log 2020-07-18 01:11:32.039426089 +0000 +++ b2/build.log 2020-07-18 01:28:28.552126261 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Jul 17 12:31:56 -12 2020 -I: pbuilder-time-stamp: 1595032316 +I: Current time: Sat Jul 18 15:11:59 +14 2020 +I: pbuilder-time-stamp: 1595034719 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Tue Sep 4 01:22:38 2018 -12 +gpgv: Signature made Wed Sep 5 03:22:38 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking garli_2.1-3.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/16347/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/27629/tmp/hooks/D01_modify_environment starting +debug: Running on odxu4b. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/27629/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/27629/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='d809cce7b37e4113bb7364420cbf7f1c' - 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='16347' - PS1='# ' - PS2='> ' + INVOCATION_ID=e74bf90ae7e04730b3a1ad7fa0b66572 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=27629 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/tmp.c7EaQunS6l/pbuilderrc_V1Y2 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c7EaQunS6l/b1 --logfile b1/build.log garli_2.1-3.dsc' - SUDO_GID='115' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.c7EaQunS6l/pbuilderrc_hXWZ --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.c7EaQunS6l/b2 --logfile b2/build.log garli_2.1-3.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux p64b 4.19.0-9-arm64 #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 4.19.0-9-armmp-lpae #1 SMP Debian 4.19.118-2+deb10u1 (2020-06-07) armv7l GNU/Linux I: ls -l /bin total 3328 - -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat - -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown - -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp - -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash - -rwxr-xr-x 1 root root 71648 Feb 28 2019 date - -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd - -rwxr-xr-x 1 root root 55672 Feb 28 2019 df - -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir - -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 18260 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount - -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln - -rwxr-xr-x 1 root root 34932 Jul 26 2018 login - -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls - -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 26024 Jan 9 2019 more - -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount - -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm - -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 15 21:16 sh -> dash - -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty - -rwsr-xr-x 1 root root 42472 Jan 9 2019 su - -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync - -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar - -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch - -rwxr-xr-x 1 root root 18260 Feb 28 2019 true - -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server - -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount - -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/16347/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat + -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown + -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp + -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash + -rwxr-xr-x 1 root root 71648 Mar 1 2019 date + -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd + -rwxr-xr-x 1 root root 55672 Mar 1 2019 df + -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir + -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 18260 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount + -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln + -rwxr-xr-x 1 root root 34932 Jul 27 2018 login + -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls + -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 26024 Jan 10 2019 more + -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount + -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm + -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 18 15:12 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 15 22:28 sh.distrib -> dash + -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty + -rwsr-xr-x 1 root root 42472 Jan 10 2019 su + -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync + -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar + -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch + -rwxr-xr-x 1 root root 18260 Mar 1 2019 true + -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server + -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount + -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/27629/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -270,7 +304,7 @@ Get: 68 http://deb.debian.org/debian buster/main armhf openmpi-bin armhf 3.1.3-11 [198 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libopenmpi-dev armhf 3.1.3-11 [964 kB] Get: 70 http://deb.debian.org/debian buster/main armhf ncl-tools armhf 2.1.21+git20180827.c71b264-2 [136 kB] -Fetched 28.0 MB in 6s (4684 kB/s) +Fetched 28.0 MB in 3s (8709 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (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 ... 18932 files and directories currently installed.) @@ -576,7 +610,7 @@ fakeroot is already the newest version (1.23-1). 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 +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 dpkg-buildpackage: info: source package garli dpkg-buildpackage: info: source version 2.1-3 dpkg-buildpackage: info: source distribution unstable @@ -639,8 +673,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -719,7 +753,7 @@ config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode dh_auto_build - make -j3 + make -j6 make[2]: Entering directory '/build/garli-2.1' make all-recursive make[3]: Entering directory '/build/garli-2.1' @@ -729,6 +763,8 @@ mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp +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 datamatr.o datamatr.cpp adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char *) this, 1, scalarSize, in); @@ -790,8 +826,9 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.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 datamatr.o datamatr.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 funcs.o funcs.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 garlimain.o garlimain.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 garlireader.o garlireader.cpp configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': configoptions.cpp:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] sprintf(modName, "model%d", modelNum); @@ -813,7 +850,13 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 funcs.o funcs.cpp +garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] + outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + ^~~~~~~~ +garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] + outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); + ^~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(&ch, sizeof(char), 1, file); @@ -825,15 +868,8 @@ datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] fscanf(inf, "%d %d", &num_taxa, &num_chars); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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 garlimain.o garlimain.cpp -garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] - outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); - ^~~~~~~~ -garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] - outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); - ^~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o garlireader.o garlireader.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o individual.o individual.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp garlimain.cpp: In function 'int SubGarliMain(int)': garlimain.cpp:323:23: warning: '%d' directive writing between 2 and 10 bytes into a region of size 6 [-Wformat-overflow=] else sprintf(temp, ".run%d", rank); @@ -877,24 +913,6 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.h:24, - from funcs.h:25, - from individual.cpp:28: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from population.h:24, - from funcs.h:25, - from individual.cpp:28: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': @@ -932,6 +950,19 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +In file included from /usr/include/c++/8/vector:69, + from population.h:24, + from funcs.h:25, + from individual.cpp:28: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -963,6 +994,82 @@ population.cpp:1896:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(this, scalarSize, 1, pin); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from population.h:24, + from funcs.h:25, + from individual.cpp:28: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Individual::RefineStartingConditions(bool, FLOAT_TYPE)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': +tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6815:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6816:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6817:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6818:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6819:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6823:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6826:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6829:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6833:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6837:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6841:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6845:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6849:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6855:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6858:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6862:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6865:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6868:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6872:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6878:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &dum, sizeof(dum), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +tree.cpp:6881:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ population.cpp: In member function 'int Population::EvaluateStoredTrees(bool)': population.cpp:3066:19: warning: '%d' directive writing between 1 and 9 bytes into a region of size 8 [-Wformat-overflow=] sprintf(oStr, "R(%d)", d + 1); @@ -979,41 +1086,89 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __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 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 mpitrick.o mpitrick.cpp In file included from /usr/include/c++/8/vector:69, - from model.h:28, - from model.cpp:25: + from population.cpp:23: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, - from model.h:28, - from model.cpp:25: -/usr/include/c++/8/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': + from population.cpp:23: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from population.cpp:23: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 +In file included from /usr/include/c++/8/vector:64, + from population.cpp:23: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from population.cpp:23: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from model.h:28, + from model.cpp:25: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +In file included from /usr/include/c++/8/vector:64, + from model.h:28, + from model.cpp:25: +/usr/include/c++/8/bits/stl_vector.h: In constructor 'BaseParameter::BaseParameter(const char*, FLOAT_TYPE**, int, int, FLOAT_TYPE, FLOAT_TYPE, int)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from population.cpp:23: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from population.cpp:23: +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from population.cpp:23: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from population.cpp:23: +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +/usr/include/c++/8/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from model.h:28, from model.cpp:25: @@ -1022,10 +1177,6 @@ vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'void Model::CalcSynonymousBranchlengthProportions(std::vector&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -1078,123 +1229,6 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector >::iterator' {aka '__gnu_cxx::__normal_iterator*, std::vector > >'} changed in GCC 7.1 -In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::OptimizeSiteRates()': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -mpic++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -DSUBROUTINE_GARLI -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp -tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': -tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6815:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &lnL, sizeof(FLOAT_TYPE), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6816:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &numTipsAdded, sizeof(numTipsAdded), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6817:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &numNodesAdded, sizeof(numNodesAdded), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6818:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &numBranchesAdded, sizeof(numBranchesAdded), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6819:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &numNodesTotal, sizeof(numNodesTotal), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6823:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6826:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6829:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6833:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6837:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6841:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &allNodes[0]->dlen, sizeof(FLOAT_TYPE), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6845:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6849:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6855:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6858:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&(allNodes[i]->dlen), sizeof(FLOAT_TYPE), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6862:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6865:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6868:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6872:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6878:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &dum, sizeof(dum), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -tree.cpp:6881:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread((char*) &allNodes[i]->dlen, sizeof(FLOAT_TYPE), 1, in); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mpic++ -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 -Wl,-z,relro -Wl,-z,now -L/usr/lib -Wl,-z,relro -Wl,-z,now -L/usr/lib -o Garli adaptation.o bipartition.o condlike.o configoptions.o configreader.o datamatr.o funcs.o garlimain.o garlireader.o individual.o linalg.o model.o optimization.o population.o rng.o sequencedata.o set.o translatetable.o tree.o treenode.o mpitrick.o -lncl -lncl make[4]: Leaving directory '/build/garli-2.1/src' Making all in tests @@ -1270,8 +1304,8 @@ checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes -checking whether UID '1111' is supported by ustar format... yes -checking whether GID '1111' is supported by ustar format... yes +checking whether UID '2222' is supported by ustar format... yes +checking whether GID '2222' is supported by ustar format... yes checking how to create a ustar tar archive... gnutar checking whether ln -s works... yes checking for gcc... gcc @@ -1348,7 +1382,7 @@ configure: WARNING: unrecognized options: --disable-maintainer-mode make[1]: Leaving directory '/build/garli-2.1' dh_auto_build - make -j3 + make -j6 make[1]: Entering directory '/build/garli-2.1' make all-recursive make[2]: Entering directory '/build/garli-2.1' @@ -1358,6 +1392,34 @@ g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o bipartition.o bipartition.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o condlike.o condlike.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configoptions.o configoptions.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.cpp +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 datamatr.o datamatr.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 funcs.o funcs.cpp +datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': +datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] + fscanf(inf, "%d %d", &num_taxa, &num_chars); + ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': +configoptions.cpp:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] + sprintf(modName, "model%d", modelNum); + ^~~~~~~~~ +configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] +In file included from /usr/include/stdio.h:873, + from /usr/include/c++/8/cstdio:42, + from /usr/include/c++/8/ext/string_conversions.h:43, + from /usr/include/c++/8/bits/basic_string.h:6400, + from /usr/include/c++/8/string:52, + from /usr/include/c++/8/bits/locale_classes.h:40, + from /usr/include/c++/8/bits/ios_base.h:41, + from /usr/include/c++/8/ios:42, + from /usr/include/c++/8/ostream:38, + from /usr/include/c++/8/iostream:39, + from configoptions.cpp:20: +/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 + return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, + ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + __bos (__s), __fmt, __va_arg_pack ()); + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ adaptation.cpp: In member function 'void Adaptation::ReadFromCheckpoint(FILE*)': adaptation.cpp:271:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char *) this, 1, scalarSize, in); @@ -1419,50 +1481,24 @@ adaptation.cpp:305:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char *) anyModelnum, sizeof(int), intervalsToStore, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o configreader.o configreader.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 datamatr.o datamatr.cpp -configoptions.cpp: In member function 'bool GeneralGamlConfig::ReadPossibleModelPartition(ConfigReader&)': -configoptions.cpp:337:20: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=] - sprintf(modName, "model%d", modelNum); - ^~~~~~~~~ -configoptions.cpp:337:20: note: directive argument in the range [0, 2147483647] -In file included from /usr/include/stdio.h:873, - from /usr/include/c++/8/cstdio:42, - from /usr/include/c++/8/ext/string_conversions.h:43, - from /usr/include/c++/8/bits/basic_string.h:6400, - from /usr/include/c++/8/string:52, - from /usr/include/c++/8/bits/locale_classes.h:40, - from /usr/include/c++/8/bits/ios_base.h:41, - from /usr/include/c++/8/ios:42, - from /usr/include/c++/8/ostream:38, - from /usr/include/c++/8/iostream:39, - from configoptions.cpp:20: -/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 7 and 16 bytes into a destination of size 10 - return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, - ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - __bos (__s), __fmt, __va_arg_pack ()); - ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o funcs.o funcs.cpp -configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': -configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&ch, sizeof(char), 1, file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] - fread(&ch, sizeof(char), 1, file); - ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ -datamatr.cpp: In member function 'int DataMatrix::ReadPhylip(const char*)': -datamatr.cpp:1390:8: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result] - fscanf(inf, "%d %d", &num_taxa, &num_chars); - ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 garlimain.o garlimain.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 garlireader.o garlireader.cpp garlimain.cpp:434:45: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ garlimain.cpp:434:55: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time] outman.UserMessageNoCR("Compiled %s %s", __DATE__, __TIME__); ^~~~~~~~ -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 garlireader.o garlireader.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 individual.o individual.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 linalg.o linalg.cpp +configreader.cpp: In member function 'int ConfigReader::ReadLine(FILE*, std::__cxx11::string&)': +configreader.cpp:602:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&ch, sizeof(char), 1, file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +configreader.cpp:605:8: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] + fread(&ch, sizeof(char), 1, file); + ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp In file included from /usr/include/c++/8/vector:69, from population.h:24, from funcs.h:25, @@ -1479,8 +1515,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o linalg.o linalg.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o model.o model.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o optimization.o optimization.cpp g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o population.o population.cpp model.cpp: In member function 'void Model::ReadBinaryFormattedModel(FILE*)': @@ -1518,6 +1552,8 @@ model.cpp:4956:9: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread(dummy, sizeof(FLOAT_TYPE), 1, in); ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp In file included from tree.h:35, from individual.h:21, from population.h:31, @@ -1565,14 +1601,26 @@ ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o rng.o rng.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o sequencedata.o sequencedata.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp In file included from /usr/include/c++/8/vector:69, from population.cpp:23: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from population.cpp:23: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); + ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from model.h:28, from model.cpp:25: @@ -1587,16 +1635,6 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::BetterFinalOptimization()': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::InitialOptimization(Individual*, bool, FLOAT_TYPE)': -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void ModelPartition::ReadModelPartitionCheckpoint(FILE*)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); @@ -1629,16 +1667,6 @@ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ -/usr/include/c++/8/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::__cxx11::string&)': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:64, - from model.h:28, - from model.cpp:25: -/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), __x); - ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from population.cpp:23: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -1652,19 +1680,8 @@ /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: -/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 - vector<_Tp, _Alloc>:: - ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/8/vector:69, - from model.h:28, - from model.cpp:25: -/usr/include/c++/8/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); - ^~~~~~~~~~~~~~~~~ +g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +/usr/include/c++/8/bits/vector.tcc: In member function 'void ModelPartition::ReadGarliFormattedModelStrings(std::__cxx11::string&)': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ @@ -1675,17 +1692,24 @@ _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, - from model.h:28, - from model.cpp:25: -/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - _M_realloc_insert(end(), std::forward<_Args>(__args)...); + from population.cpp:23: +/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 + vector<_Tp, _Alloc>:: + ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:64, + from population.cpp:23: +/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': +/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/8/vector:69, + from population.cpp:23: /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from population.cpp:23: -/usr/include/c++/8/bits/stl_vector.h: In member function 'void Population::VariableStartingTreeOptimization(bool)': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ @@ -1700,20 +1724,30 @@ _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, - from population.cpp:23: + from model.h:28, + from model.cpp:25: +/usr/include/c++/8/bits/vector.tcc: In constructor 'ModelPartition::ModelPartition()': +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, - from population.cpp:23: + from model.h:28, + from model.cpp:25: /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o set.o set.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o translatetable.o translatetable.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o tree.o tree.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o treenode.o treenode.cpp -g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -I/usr/include/ncl -DIGNORE_NXS_ASSERT -g -O2 -ffile-prefix-map=/build/garli-2.1=. -fstack-protector-strong -Wformat -Werror=format-security -DUNIX -DNCL_CONST_FUNCS -DNDEBUG -Wno-uninitialized -fsigned-char -O3 -ffast-math -funroll-loops -fstrict-aliasing -c -o mpitrick.o mpitrick.cpp +In file included from /usr/include/c++/8/vector:69, + from model.h:28, + from model.cpp:25: +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ +/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + _M_realloc_insert(end(), std::forward<_Args>(__args)...); + ^~~~~~~~~~~~~~~~~ tree.cpp: In member function 'void Tree::ReadBinaryFormattedTree(FILE*)': tree.cpp:6808:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result] fread((char*) &numTipsTotal, sizeof(numTipsTotal), 1, in); @@ -1797,7 +1831,7 @@ # 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/' \{\} \; dh_auto_test - make -j3 check VERBOSE=1 + make -j6 check VERBOSE=1 make[2]: Entering directory '/build/garli-2.1' Making check in src make[3]: Entering directory '/build/garli-2.1/src' @@ -4317,7 +4351,7 @@ 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 5 seconds +Time used = 0 hours, 0 minutes and 1 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4467,7 +4501,7 @@ 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 7 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4610,7 +4644,7 @@ 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 ... ####################################################### @@ -4764,7 +4798,7 @@ pass 10: -12956.1235 (branch= 0.0000 omega= 0.0000) Looking for minimum length branches... Final score = -12956.1235 -Time used = 0 hours, 2 minutes and 27 seconds +Time used = 0 hours, 0 minutes and 50 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -4916,7 +4950,7 @@ pass 10: -13269.2298 (branch= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -13269.2298 -Time used = 0 hours, 1 minutes and 43 seconds +Time used = 0 hours, 0 minutes and 33 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5120,7 +5154,7 @@ pass 80: -3350.2338 (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 = -3350.2338 -Time used = 0 hours, 0 minutes and 8 seconds +Time used = 0 hours, 0 minutes and 4 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5328,7 +5362,7 @@ pass 75: -3325.9822 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) Looking for minimum length branches... Final score = -3325.9822 -Time used = 0 hours, 0 minutes and 11 seconds +Time used = 0 hours, 0 minutes and 6 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5490,7 +5524,7 @@ 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 4 seconds +Time used = 0 hours, 0 minutes and 2 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -5814,7 +5848,7 @@ pass 17: -14498.8854 (branch= 0.0000 eq freqs= 0.0000 rel rates= 0.0000) Looking for minimum length branches... Final score = -14498.8854 -Time used = 0 hours, 0 minutes and 50 seconds +Time used = 0 hours, 0 minutes and 23 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -6068,7 +6102,7 @@ pass 34: -13306.2065 (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 = -13306.2065 -Time used = 0 hours, 0 minutes and 41 seconds +Time used = 0 hours, 0 minutes and 23 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -7337,7 +7371,7 @@ pass 14: -464.5474 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -464.5474 -Time used = 0 hours, 0 minutes and 1 seconds +Time used = 0 hours, 0 minutes and 0 seconds Writing site likelihoods for tree 1 ... ####################################################### @@ -8039,7 +8073,7 @@ pass 495: -208.3583 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0001) Looking for minimum length branches... Final score = -208.3583 -Time used = 0 hours, 0 minutes and 30 seconds +Time used = 0 hours, 0 minutes and 7 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8303,7 +8337,7 @@ pass 375: -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 32 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8593,7 +8627,7 @@ pass 498: -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 25 seconds +Time used = 0 hours, 0 minutes and 11 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -8886,7 +8920,7 @@ pass 500: -208.3575 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002) Looking for minimum length branches... Final score = -208.3575 -Time used = 0 hours, 0 minutes and 30 seconds +Time used = 0 hours, 0 minutes and 9 seconds MODEL REPORT - Parameter values are FINAL Model 1 @@ -11591,6 +11625,9 @@ gen current_lnL precision last_tree_imp 0 -103.2377 0.500 0 100 -102.5786 0.500 81 +200 -100.8816 0.500 183 +300 -100.5813 0.500 183 +400 -100.3300 0.500 183 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -11687,12 +11724,9 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 139, seed 1972683460, best lnL -102.344 +Bootstrap rep 1 (of 1) generation 435, seed 1578646324, best lnL -100.164 gen current_lnL precision last_tree_imp -139 -102.3439 0.500 81 -200 -100.8816 0.500 183 -300 -100.5813 0.500 183 -400 -100.3300 0.500 183 +435 -100.1636 0.500 183 500 -100.0135 0.500 183 600 -99.2983 0.500 549 700 -99.1955 0.500 549 @@ -11952,9 +11986,9 @@ STARTING RUN Restarting from checkpoint... - generation 109, seed 1623716043, best lnL -112.907 + generation 107, seed 1108278274, best lnL -112.907 gen current_lnL precision last_tree_imp -109 -112.9066 0.500 84 +107 -112.9066 0.500 84 200 -112.4964 0.500 84 300 -112.3224 0.500 84 400 -112.1061 0.500 84 @@ -12134,6 +12168,16 @@ 200 -112.5462 0.500 160 300 -112.1250 0.500 160 400 -111.8851 0.500 160 +500 -111.7755 0.500 160 +600 -111.6975 0.500 563 +700 -111.6876 0.500 563 +800 -111.6844 0.500 563 +900 -111.6835 0.500 563 +1000 -111.6829 0.500 563 +1100 -111.6827 0.500 563 +Optimization precision reduced + Optimizing parameters... improved 0.000 lnL + Optimizing branchlengths... improved 0.000 lnL NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12219,18 +12263,11 @@ STARTING RUN Restarting from checkpoint... - generation 446, seed 1357591034, best lnL -111.830 + generation 1140, seed 449245285, best lnL -111.683 gen current_lnL precision last_tree_imp -446 -111.8297 0.500 160 -500 -111.7755 0.500 160 -600 -111.6975 0.500 563 -700 -111.6876 0.500 563 -800 -111.6844 0.500 563 -900 -111.6835 0.500 563 -1000 -111.6829 0.500 563 -NOTE: ****Specified generation limit (1000) reached... +1140 -111.6826 0.010 563 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING GENERATION LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 20 (amino acid data) Amino Acid Rate Matrix: Jones @@ -12247,30 +12284,23 @@ No branches were short enough to be collapsed. Saving site likelihoods to file ch.a.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -111.6829 +Replicate 1 : -111.6826 Parameter estimates: Model contains no estimated parameters Treelengths: TL -rep 1: 2.616 +rep 1: 2.621 Saving final tree from best search rep (#1) to ch.a.best.tre Inferring internal state probabilities on best tree... saving to file ch.a.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/c.M3x2.conf @@ -12393,6 +12423,7 @@ lnL after optimization: -208.9856 gen current_lnL precision last_tree_imp 0 -208.9856 0.500 0 +10 -207.1401 0.500 10 NOTE: ****Specified time limit (10 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -12479,10 +12510,9 @@ STARTING RUN Restarting from checkpoint... - generation 1, seed 1398556760, best lnL -208.980 + generation 16, seed 1304835690, best lnL -206.434 gen current_lnL precision last_tree_imp -1 -208.9797 0.500 0 -10 -207.1401 0.500 10 +16 -206.4341 0.500 13 20 -205.6892 0.500 18 30 -205.6499 0.500 18 40 -205.6371 0.500 18 @@ -13077,9 +13107,9 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 297, seed 1638204839, best lnL -3356.591 +Search rep 1 (of 2) generation 227, seed 1946944422, best lnL -3356.684 gen current_lnL precision last_tree_imp -297 -3356.5910 0.500 0 +227 -3356.6840 0.500 0 300 -3356.5910 0.500 0 400 -3355.9752 0.500 0 500 -3355.8101 0.500 0 @@ -13087,64 +13117,72 @@ Optimizing parameters... improved 0.940 lnL Optimizing branchlengths... improved 0.000 lnL 600 -3354.6612 0.255 0 +700 -3354.3974 0.255 0 +800 -3354.0880 0.255 0 +900 -3353.8938 0.255 0 +1000 -3353.6942 0.255 0 +Optimization precision reduced + Optimizing parameters... improved 0.828 lnL + Optimizing branchlengths... improved 0.083 lnL +1100 -3352.7289 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3354.4030 +Current score = -3352.7285 Performing final optimizations... -pass 1 : -3353.4346 (branch= 0.1147 alpha= 0.0000 pinv= 0.0329 eq freqs= 0.0670 rel rates= 0.6968 subset rates= 0.0569) -pass 2 : -3352.7859 (branch= 0.1146 alpha= 0.0031 pinv= 0.0173 eq freqs= 0.0216 rel rates= 0.4557 subset rates= 0.0364) -pass 3 : -3352.3005 (branch= 0.0745 alpha= 0.0093 pinv= 0.0163 eq freqs= 0.0056 rel rates= 0.3589 subset rates= 0.0206) -pass 4 : -3351.9350 (branch= 0.0434 alpha= 0.0084 pinv= 0.0160 eq freqs= 0.0032 rel rates= 0.2824 subset rates= 0.0121) -pass 5 : -3351.6330 (branch= 0.0286 alpha= 0.0095 pinv= 0.0153 eq freqs= 0.0014 rel rates= 0.2408 subset rates= 0.0065) -pass 6 : -3351.3951 (branch= 0.0148 alpha= 0.0099 pinv= 0.0145 eq freqs= 0.0006 rel rates= 0.1934 subset rates= 0.0047) -pass 7 : -3351.2052 (branch= 0.0081 alpha= 0.0112 pinv= 0.0135 eq freqs= 0.0007 rel rates= 0.1530 subset rates= 0.0034) -pass 8 : -3351.0486 (branch= 0.0065 alpha= 0.0101 pinv= 0.0125 eq freqs= 0.0005 rel rates= 0.1254 subset rates= 0.0016) -pass 9 : -3350.9215 (branch= 0.0042 alpha= 0.0100 pinv= 0.0115 eq freqs= 0.0004 rel rates= 0.1010 subset rates= 0.0000) -pass 10: -3350.8133 (branch= 0.0009 alpha= 0.0099 pinv= 0.0111 eq freqs= 0.0003 rel rates= 0.0841 subset rates= 0.0019) -pass 11: -3350.7258 (branch= 0.0019 alpha= 0.0095 pinv= 0.0101 eq freqs= 0.0003 rel rates= 0.0657 subset rates= 0.0000) -pass 12: -3350.6544 (branch= 0.0004 alpha= 0.0085 pinv= 0.0085 eq freqs= 0.0001 rel rates= 0.0539 subset rates= 0.0000) -pass 13: -3350.5921 (branch= 0.0001 alpha= 0.0082 pinv= 0.0077 eq freqs= 0.0001 rel rates= 0.0449 subset rates= 0.0012) -pass 14: -3350.5413 (branch= 0.0007 alpha= 0.0073 pinv= 0.0070 eq freqs= 0.0002 rel rates= 0.0356 subset rates= 0.0000) -pass 15: -3350.4988 (branch= 0.0002 alpha= 0.0065 pinv= 0.0062 eq freqs= 0.0001 rel rates= 0.0295 subset rates= 0.0000) -pass 16: -3350.4621 (branch= 0.0001 alpha= 0.0061 pinv= 0.0056 eq freqs= 0.0001 rel rates= 0.0249 subset rates= 0.0000) -pass 17: -3350.4304 (branch= 0.0000 alpha= 0.0055 pinv= 0.0050 eq freqs= 0.0001 rel rates= 0.0212 subset rates= 0.0000) -pass 18: -3350.4032 (branch= 0.0000 alpha= 0.0049 pinv= 0.0044 eq freqs= 0.0001 rel rates= 0.0177 subset rates= 0.0000) -pass 19: -3350.3798 (branch= 0.0000 alpha= 0.0043 pinv= 0.0039 eq freqs= 0.0001 rel rates= 0.0151 subset rates= 0.0000) -pass 20: -3350.3596 (branch= 0.0000 alpha= 0.0038 pinv= 0.0035 eq freqs= 0.0000 rel rates= 0.0128 subset rates= 0.0000) - optimization up to ... -pass 30: -3350.2622 (branch= 0.0000 alpha= 0.0197 pinv= 0.0180 eq freqs= 0.0001 rel rates= 0.0596 subset rates= 0.0000) - optimization up to ... -pass 40: -3350.2400 (branch= 0.0000 alpha= 0.0044 pinv= 0.0041 eq freqs= 0.0000 rel rates= 0.0136 subset rates= 0.0000) +pass 1 : -3352.3450 (branch= 0.0085 alpha= 0.0082 pinv= 0.0184 eq freqs= 0.0113 rel rates= 0.3275 subset rates= 0.0095) +pass 2 : -3351.9924 (branch= 0.0561 alpha= 0.0098 pinv= 0.0178 eq freqs= 0.0050 rel rates= 0.2507 subset rates= 0.0132) +pass 3 : -3351.7268 (branch= 0.0263 alpha= 0.0107 pinv= 0.0172 eq freqs= 0.0018 rel rates= 0.2032 subset rates= 0.0062) +pass 4 : -3351.4894 (branch= 0.0225 alpha= 0.0119 pinv= 0.0163 eq freqs= 0.0025 rel rates= 0.1785 subset rates= 0.0056) +pass 5 : -3351.3032 (branch= 0.0127 alpha= 0.0124 pinv= 0.0152 eq freqs= 0.0010 rel rates= 0.1405 subset rates= 0.0044) +pass 6 : -3351.1455 (branch= 0.0082 alpha= 0.0110 pinv= 0.0143 eq freqs= 0.0005 rel rates= 0.1208 subset rates= 0.0028) +pass 7 : -3351.0141 (branch= 0.0054 alpha= 0.0109 pinv= 0.0132 eq freqs= 0.0004 rel rates= 0.0994 subset rates= 0.0021) +pass 8 : -3350.8982 (branch= 0.0039 alpha= 0.0106 pinv= 0.0121 eq freqs= 0.0003 rel rates= 0.0874 subset rates= 0.0016) +pass 9 : -3350.8025 (branch= 0.0028 alpha= 0.0101 pinv= 0.0112 eq freqs= 0.0002 rel rates= 0.0714 subset rates= 0.0000) +pass 10: -3350.7173 (branch= 0.0006 alpha= 0.0099 pinv= 0.0108 eq freqs= 0.0002 rel rates= 0.0621 subset rates= 0.0016) +pass 11: -3350.6482 (branch= 0.0013 alpha= 0.0095 pinv= 0.0098 eq freqs= 0.0002 rel rates= 0.0483 subset rates= 0.0000) +pass 12: -3350.5900 (branch= 0.0003 alpha= 0.0084 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0411 subset rates= 0.0000) +pass 13: -3350.5388 (branch= 0.0001 alpha= 0.0081 pinv= 0.0075 eq freqs= 0.0001 rel rates= 0.0344 subset rates= 0.0011) +pass 14: -3350.4974 (branch= 0.0006 alpha= 0.0072 pinv= 0.0067 eq freqs= 0.0001 rel rates= 0.0267 subset rates= 0.0000) +pass 15: -3350.4619 (branch= 0.0001 alpha= 0.0063 pinv= 0.0060 eq freqs= 0.0000 rel rates= 0.0231 subset rates= 0.0000) +pass 16: -3350.4309 (branch= 0.0000 alpha= 0.0058 pinv= 0.0054 eq freqs= 0.0001 rel rates= 0.0197 subset rates= 0.0000) +pass 17: -3350.4039 (branch= 0.0000 alpha= 0.0053 pinv= 0.0048 eq freqs= 0.0000 rel rates= 0.0168 subset rates= 0.0000) +pass 18: -3350.3806 (branch= 0.0000 alpha= 0.0047 pinv= 0.0043 eq freqs= 0.0000 rel rates= 0.0143 subset rates= 0.0000) +pass 19: -3350.3605 (branch= 0.0000 alpha= 0.0042 pinv= 0.0038 eq freqs= 0.0000 rel rates= 0.0121 subset rates= 0.0000) +pass 20: -3350.3432 (branch= 0.0000 alpha= 0.0037 pinv= 0.0033 eq freqs= 0.0000 rel rates= 0.0103 subset rates= 0.0000) + optimization up to ... +pass 30: -3350.2584 (branch= 0.0000 alpha= 0.0189 pinv= 0.0172 eq freqs= 0.0001 rel rates= 0.0486 subset rates= 0.0000) + optimization up to ... +pass 40: -3350.2390 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0112 subset rates= 0.0000) optimization up to ... -pass 50: -3350.2350 (branch= 0.0000 alpha= 0.0008 pinv= 0.0008 eq freqs= 0.0000 rel rates= 0.0034 subset rates= 0.0000) +pass 50: -3350.2346 (branch= 0.0000 alpha= 0.0008 pinv= 0.0007 eq freqs= 0.0000 rel rates= 0.0028 subset rates= 0.0000) optimization up to ... -pass 60: -3350.2339 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0009 subset rates= 0.0000) +pass 60: -3350.2336 (branch= 0.0000 alpha= 0.0001 pinv= 0.0001 eq freqs= 0.0000 rel rates= 0.0007 subset rates= 0.0000) optimization up to ... -pass 70: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) +pass 70: -3350.2334 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 subset rates= 0.0000) optimization up to ... -pass 73: -3350.2336 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 subset rates= 0.0000) +pass 74: -3350.2334 (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 = -3350.2336 -Time used so far = 0 hours, 0 minutes and 18 seconds +Final score = -3350.2334 +Time used so far = 0 hours, 0 minutes and 14 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.107, AG = 10.384, AT = 2.680, CG = 0.001, CT = 21.824, GT = 1.000 + AC = 3.112, AG = 10.401, AT = 2.685, CG = 0.001, CT = 21.869, 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 - 0.5795 + 0.5788 with an invariant (invariable) site category, proportion estimated - 0.3663 + 0.3661 Substitution rate categories under this model: rate proportion - 0.0000 0.3663 - 0.0489 0.1584 - 0.3007 0.1584 - 0.8705 0.1584 - 2.7799 0.1584 + 0.0000 0.3661 + 0.0488 0.1585 + 0.3003 0.1585 + 0.8701 0.1585 + 2.7809 0.1585 Model 2 Number of states = 2 (binary data) @@ -13169,13 +13207,13 @@ Completed 1 replicate search(es) (of 2). Results: -Replicate 1 : -3350.2336 (best) (TERMINATED PREMATURELY) +Replicate 1 : -3350.2334 (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: 3.107 10.38 2.68 0.001 21.82 1 0.333 0.222 0.157 0.288 0.580 0.366 +rep 1: 3.112 10.4 2.685 0.001 21.87 1 0.333 0.222 0.157 0.288 0.579 0.366 Partition model subset 2: Model contains no estimated parameters @@ -13428,68 +13466,69 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 2) generation 82, seed 920432122, best lnL -3325.087 +Search rep 1 (of 2) generation 79, seed 2116197142, best lnL -3325.087 gen current_lnL precision last_tree_imp -82 -3325.0865 0.500 1 +79 -3325.0865 0.500 1 100 -3324.9856 0.500 1 +200 -3324.7543 0.500 1 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -3324.8133 +Current score = -3324.7364 Performing final optimizations... -pass 1 : -3321.6345 (branch= 0.9446 alpha= 0.0128 pinv= 0.0156 eq freqs= 0.0976 rel rates= 0.8050 ins/del rates= 1.3031) -pass 2 : -3320.5969 (branch= 0.4000 alpha= 0.0000 pinv= 0.0202 eq freqs= 0.0115 rel rates= 0.5711 ins/del rates= 0.0349) -pass 3 : -3320.0256 (branch= 0.0948 alpha= 0.0072 pinv= 0.0165 eq freqs= 0.0085 rel rates= 0.4185 ins/del rates= 0.0257) -pass 4 : -3319.6007 (branch= 0.0399 alpha= 0.0101 pinv= 0.0157 eq freqs= 0.0035 rel rates= 0.3420 ins/del rates= 0.0138) -pass 5 : -3319.2690 (branch= 0.0226 alpha= 0.0097 pinv= 0.0152 eq freqs= 0.0011 rel rates= 0.2739 ins/del rates= 0.0090) -pass 6 : -3319.0187 (branch= 0.0137 alpha= 0.0109 pinv= 0.0144 eq freqs= 0.0012 rel rates= 0.2045 ins/del rates= 0.0058) -pass 7 : -3318.8149 (branch= 0.0091 alpha= 0.0104 pinv= 0.0136 eq freqs= 0.0005 rel rates= 0.1662 ins/del rates= 0.0039) -pass 8 : -3318.6494 (branch= 0.0060 alpha= 0.0109 pinv= 0.0126 eq freqs= 0.0006 rel rates= 0.1328 ins/del rates= 0.0025) -pass 9 : -3318.5149 (branch= 0.0039 alpha= 0.0104 pinv= 0.0117 eq freqs= 0.0004 rel rates= 0.1065 ins/del rates= 0.0017) -pass 10: -3318.4039 (branch= 0.0025 alpha= 0.0101 pinv= 0.0115 eq freqs= 0.0003 rel rates= 0.0854 ins/del rates= 0.0011) -pass 11: -3318.3121 (branch= 0.0017 alpha= 0.0095 pinv= 0.0106 eq freqs= 0.0002 rel rates= 0.0692 ins/del rates= 0.0007) -pass 12: -3318.2366 (branch= 0.0011 alpha= 0.0088 pinv= 0.0091 eq freqs= 0.0002 rel rates= 0.0558 ins/del rates= 0.0005) -pass 13: -3318.1734 (branch= 0.0007 alpha= 0.0082 pinv= 0.0083 eq freqs= 0.0001 rel rates= 0.0455 ins/del rates= 0.0003) -pass 14: -3318.1196 (branch= 0.0005 alpha= 0.0076 pinv= 0.0075 eq freqs= 0.0001 rel rates= 0.0379 ins/del rates= 0.0002) -pass 15: -3318.0737 (branch= 0.0003 alpha= 0.0070 pinv= 0.0068 eq freqs= 0.0001 rel rates= 0.0315 ins/del rates= 0.0001) -pass 16: -3318.0349 (branch= 0.0002 alpha= 0.0065 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0257 ins/del rates= 0.0001) -pass 17: -3318.0017 (branch= 0.0001 alpha= 0.0059 pinv= 0.0055 eq freqs= 0.0001 rel rates= 0.0216 ins/del rates= 0.0000) -pass 18: -3317.9730 (branch= 0.0001 alpha= 0.0053 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0184 ins/del rates= 0.0000) -pass 19: -3317.9481 (branch= 0.0001 alpha= 0.0047 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0156 ins/del rates= 0.0000) -pass 20: -3317.9265 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0133 ins/del rates= 0.0000) +pass 1 : -3321.6302 (branch= 0.9208 alpha= 0.0108 pinv= 0.0166 eq freqs= 0.0473 rel rates= 0.7947 ins/del rates= 1.3161) +pass 2 : -3320.5348 (branch= 0.3783 alpha= 0.0000 pinv= 0.0229 eq freqs= 0.0240 rel rates= 0.6260 ins/del rates= 0.0441) +pass 3 : -3319.9805 (branch= 0.0886 alpha= 0.0104 pinv= 0.0160 eq freqs= 0.0102 rel rates= 0.4068 ins/del rates= 0.0222) +pass 4 : -3319.5631 (branch= 0.0363 alpha= 0.0105 pinv= 0.0155 eq freqs= 0.0044 rel rates= 0.3382 ins/del rates= 0.0125) +pass 5 : -3319.2449 (branch= 0.0215 alpha= 0.0098 pinv= 0.0151 eq freqs= 0.0012 rel rates= 0.2619 ins/del rates= 0.0087) +pass 6 : -3318.9978 (branch= 0.0132 alpha= 0.0108 pinv= 0.0143 eq freqs= 0.0009 rel rates= 0.2023 ins/del rates= 0.0056) +pass 7 : -3318.7986 (branch= 0.0088 alpha= 0.0106 pinv= 0.0135 eq freqs= 0.0007 rel rates= 0.1620 ins/del rates= 0.0037) +pass 8 : -3318.6352 (branch= 0.0058 alpha= 0.0108 pinv= 0.0125 eq freqs= 0.0006 rel rates= 0.1312 ins/del rates= 0.0024) +pass 9 : -3318.5034 (branch= 0.0037 alpha= 0.0104 pinv= 0.0116 eq freqs= 0.0004 rel rates= 0.1041 ins/del rates= 0.0016) +pass 10: -3318.3946 (branch= 0.0025 alpha= 0.0099 pinv= 0.0114 eq freqs= 0.0003 rel rates= 0.0836 ins/del rates= 0.0011) +pass 11: -3318.3043 (branch= 0.0016 alpha= 0.0094 pinv= 0.0105 eq freqs= 0.0002 rel rates= 0.0678 ins/del rates= 0.0007) +pass 12: -3318.2306 (branch= 0.0011 alpha= 0.0088 pinv= 0.0090 eq freqs= 0.0002 rel rates= 0.0542 ins/del rates= 0.0005) +pass 13: -3318.1683 (branch= 0.0007 alpha= 0.0081 pinv= 0.0082 eq freqs= 0.0001 rel rates= 0.0448 ins/del rates= 0.0003) +pass 14: -3318.1153 (branch= 0.0005 alpha= 0.0075 pinv= 0.0074 eq freqs= 0.0001 rel rates= 0.0372 ins/del rates= 0.0002) +pass 15: -3318.0703 (branch= 0.0003 alpha= 0.0071 pinv= 0.0067 eq freqs= 0.0001 rel rates= 0.0307 ins/del rates= 0.0001) +pass 16: -3318.0323 (branch= 0.0002 alpha= 0.0063 pinv= 0.0061 eq freqs= 0.0001 rel rates= 0.0252 ins/del rates= 0.0001) +pass 17: -3317.9993 (branch= 0.0001 alpha= 0.0058 pinv= 0.0055 eq freqs= 0.0001 rel rates= 0.0214 ins/del rates= 0.0000) +pass 18: -3317.9710 (branch= 0.0001 alpha= 0.0052 pinv= 0.0049 eq freqs= 0.0000 rel rates= 0.0181 ins/del rates= 0.0000) +pass 19: -3317.9464 (branch= 0.0001 alpha= 0.0047 pinv= 0.0044 eq freqs= 0.0000 rel rates= 0.0154 ins/del rates= 0.0000) +pass 20: -3317.9252 (branch= 0.0000 alpha= 0.0042 pinv= 0.0039 eq freqs= 0.0000 rel rates= 0.0131 ins/del rates= 0.0000) optimization up to ... -pass 30: -3317.8198 (branch= 0.0001 alpha= 0.0229 pinv= 0.0211 eq freqs= 0.0001 rel rates= 0.0624 ins/del rates= 0.0000) +pass 30: -3317.8195 (branch= 0.0001 alpha= 0.0227 pinv= 0.0209 eq freqs= 0.0002 rel rates= 0.0618 ins/del rates= 0.0000) optimization up to ... -pass 40: -3317.7945 (branch= 0.0001 alpha= 0.0057 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0142 ins/del rates= 0.0000) +pass 40: -3317.7944 (branch= 0.0001 alpha= 0.0057 pinv= 0.0053 eq freqs= 0.0000 rel rates= 0.0141 ins/del rates= 0.0000) optimization up to ... -pass 50: -3317.7887 (branch= 0.0001 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) +pass 50: -3317.7887 (branch= 0.0000 alpha= 0.0012 pinv= 0.0011 eq freqs= 0.0000 rel rates= 0.0034 ins/del rates= 0.0000) optimization up to ... pass 60: -3317.7874 (branch= 0.0000 alpha= 0.0002 pinv= 0.0002 eq freqs= 0.0000 rel rates= 0.0008 ins/del rates= 0.0000) optimization up to ... -pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0001 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) +pass 70: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0002 ins/del rates= 0.0000) optimization up to ... -pass 75: -3317.7871 (branch= 0.0000 alpha= 0.0000 pinv= 0.0000 eq freqs= 0.0000 rel rates= 0.0000 ins/del rates= 0.0000) +pass 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 = -3317.7871 -Time used so far = 0 hours, 0 minutes and 21 seconds +Time used so far = 0 hours, 0 minutes and 25 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 3.066, AG = 10.263, AT = 2.656, CG = 0.001, CT = 21.537, GT = 1.000 + AC = 3.067, AG = 10.265, AT = 2.655, CG = 0.001, CT = 21.540, 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 - 0.5753 + 0.5750 with an invariant (invariable) site category, proportion estimated - 0.3615 + 0.3614 Substitution rate categories under this model: rate proportion - 0.0000 0.3615 + 0.0000 0.3614 0.0480 0.1596 - 0.2982 0.1596 - 0.8682 0.1596 - 2.7856 0.1596 + 0.2981 0.1596 + 0.8680 0.1596 + 2.7859 0.1596 Model 2 Number of states = 2 (0/1 coding of gaps) @@ -13521,7 +13560,7 @@ Partition model subset 1: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 3.066 10.26 2.656 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 +rep 1: 3.067 10.26 2.655 0.001 21.54 1 0.333 0.222 0.157 0.288 0.575 0.361 Partition model subset 2: ins del @@ -13653,6 +13692,18 @@ 1200 -211.1651 0.010 1104 1400 -211.1317 0.010 1104 1600 -211.0217 0.010 1104 +1800 -210.9996 0.010 1104 +2000 -210.9459 0.010 1104 +2200 -210.8945 0.010 1104 +2400 -210.8863 0.010 1104 +2600 -210.8436 0.010 1104 +2800 -210.8250 0.010 1104 +3000 -210.8189 0.010 1104 +3200 -210.7905 0.010 1104 +3400 -210.7553 0.010 1104 +3600 -210.7287 0.010 1104 +3800 -210.7083 0.010 1104 +4000 -210.6947 0.010 1104 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -13732,74 +13783,55 @@ STARTING RUN Restarting from checkpoint... - generation 1687, seed 636573060, best lnL -211.015 + generation 4026, seed 1616879158, best lnL -210.695 gen current_lnL precision last_tree_imp -1687 -211.0145 0.010 1104 -1700 -211.0090 0.010 1104 -1800 -210.9996 0.010 1104 -1900 -210.9491 0.010 1104 -2000 -210.9459 0.010 1104 -2100 -210.9365 0.010 1104 -2200 -210.8945 0.010 1104 -2300 -210.8921 0.010 1104 -2400 -210.8863 0.010 1104 -2500 -210.8674 0.010 1104 -2600 -210.8436 0.010 1104 -2700 -210.8340 0.010 1104 -2800 -210.8250 0.010 1104 -2900 -210.8229 0.010 1104 -3000 -210.8189 0.010 1104 -3100 -210.8049 0.010 1104 -NOTE: ****Specified time limit (5 seconds) reached... +4026 -210.6946 0.010 1104 +4100 -210.6827 0.010 1104 +Reached termination condition! +last topological improvement at gen 1104 +Improvement over last 500 gen = 0.04599 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.192, AG = 4.313, AT = 0.241, CG = 3.799, CT = 6.195, GT = 1.000 + AC = 2.570, AG = 4.753, AT = 0.222, CG = 4.460, CT = 6.970, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2299 0.3376 0.2132 0.2194 + (ACGT) 0.2329 0.3364 0.2106 0.2201 Rate Heterogeneity Model: 3 discrete gamma distributed rate categories, alpha param estimated - 1.1009 + 1.1902 with an invariant (invariable) site category, proportion estimated - 0.1054 + 0.1148 Substitution rate categories under this model: rate proportion - 0.0000 0.1054 - 0.2110 0.2982 - 0.7362 0.2982 - 2.0528 0.2982 + 0.0000 0.1148 + 0.2293 0.2951 + 0.7543 0.2951 + 2.0164 0.2951 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 1 branches were collapsed. + No branches were short enough to be collapsed. Saving site likelihoods to file ch.n.G3.sitelikes.log ... -WARNING: Site likelihoods being output on prematurely terminated search ... - -NOTE: ***Search was terminated before full auto-termination condition was reached! -Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** - ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -210.8049 (TERMINATED PREMATURELY) +Replicate 1 : -210.6827 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) alpha pinv -rep 1: 2.192 4.313 0.2407 3.799 6.195 1 0.230 0.338 0.213 0.219 1.101 0.105 +rep 1: 2.57 4.753 0.2216 4.46 6.97 1 0.233 0.336 0.211 0.220 1.190 0.115 Treelengths: TL -rep 1: 2.234 +rep 1: 2.232 Saving final tree from best search rep (#1) to ch.n.G3.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.G3.internalstates.log -WARNING: Internal states inferred on tree from prematurely terminated search - ####################################################### TREEFILES PASS Running checkpoint test ./check/n.G4.conf @@ -13925,6 +13957,19 @@ 1400 -191.5430 0.010 1238 1600 -191.4264 0.010 1238 1800 -191.2929 0.010 1238 +2000 -191.1582 0.010 1979 +2200 -191.0941 0.010 1979 +2400 -190.9584 0.010 1979 +2600 -190.9306 0.010 1979 +2800 -190.8937 0.010 1979 +3000 -190.8747 0.010 1979 +3200 -190.8649 0.010 1979 +3400 -190.8495 0.010 1979 +3600 -190.8373 0.010 1979 +3800 -190.7696 0.010 1979 +4000 -190.7610 0.010 1979 +4200 -190.7108 0.010 1979 +4400 -190.6941 0.010 1979 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14005,72 +14050,58 @@ Subset 1: Random seed for bootstrap reweighting: 1 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 1976, seed 204832945, best lnL -191.177 +Bootstrap rep 1 (of 1) generation 4452, seed 447742264, best lnL -190.670 gen current_lnL precision last_tree_imp -1976 -191.1768 0.010 1238 -2000 -191.1582 0.010 1979 -2100 -191.1053 0.010 1979 -2200 -191.0941 0.010 1979 -2300 -190.9736 0.010 1979 -2400 -190.9584 0.010 1979 -2500 -190.9505 0.010 1979 -2600 -190.9306 0.010 1979 -2700 -190.9080 0.010 1979 -2800 -190.8937 0.010 1979 -2900 -190.8879 0.010 1979 -3000 -190.8747 0.010 1979 -3100 -190.8661 0.010 1979 -3200 -190.8649 0.010 1979 -3300 -190.8613 0.010 1979 -3400 -190.8495 0.010 1979 -NOTE: ****Specified time limit (5 seconds) reached... +4452 -190.6698 0.010 1979 +4500 -190.6698 0.010 1979 +4600 -190.6596 0.010 1979 +4700 -190.6594 0.010 1979 +4800 -190.6554 0.010 1979 +Reached termination condition! +last topological improvement at gen 1979 +Improvement over last 500 gen = 0.04442 -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 0.461, AG = 1.077, AT = 0.009, CG = 2.177, CT = 8.929, GT = 1.000 + AC = 0.525, AG = 1.103, AT = 0.009, CG = 2.352, CT = 10.993, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.3094 0.3290 0.2513 0.1102 + (ACGT) 0.3118 0.3242 0.2589 0.1052 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated - 5.6416 + 6.3163 with an invariant (invariable) site category, proportion estimated - 0.1316 + 0.1380 Substitution rate categories under this model: rate proportion - 0.0000 0.1316 - 0.5267 0.2171 - 0.8179 0.2171 - 1.0820 0.2171 - 1.5734 0.2171 + 0.0000 0.1380 + 0.5490 0.2155 + 0.8299 0.2155 + 1.0805 0.2155 + 1.5405 0.2155 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!*** + 1 branches were collapsed. ####################################################### Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -190.8454 (TERMINATED PREMATURELY) +Replicate 1 : -190.6554 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: 0.4607 1.077 0.008854 2.177 8.929 1 0.309 0.329 0.251 0.110 5.642 0.132 +rep 1: 0.5249 1.103 0.00911 2.352 10.99 1 0.312 0.324 0.259 0.105 6.316 0.138 Treelengths: TL -rep 1: 2.226 +rep 1: 2.271 Saving best tree to bootstrap file ch.n.G4.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file +>>>Completed Bootstrap rep 1<<< ####################################################### TREEFILES PASS Running checkpoint test ./check/n.conf @@ -14185,6 +14216,21 @@ 2400 -213.2444 0.010 530 2600 -213.2281 0.010 530 2800 -213.2193 0.010 530 +3000 -213.2001 0.010 530 +3200 -213.1945 0.010 530 +3400 -213.1681 0.010 530 +3600 -213.1580 0.010 530 +3800 -213.0251 0.010 3769 +4000 -212.9703 0.010 3769 +4200 -212.9482 0.010 3769 +4400 -212.9233 0.010 3769 +4600 -212.8793 0.010 3769 +4800 -212.8765 0.010 3769 +5000 -212.8760 0.010 3769 +5200 -212.8555 0.010 3769 +5400 -212.8533 0.010 3769 +5600 -212.8185 0.010 3769 +5800 -212.7685 0.010 3769 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14264,28 +14310,30 @@ STARTING RUN Restarting from checkpoint... - generation 2958, seed 1189183913, best lnL -213.200 + generation 5888, seed 2061399910, best lnL -212.727 gen current_lnL precision last_tree_imp -2958 -213.2001 0.010 530 -3000 -213.2001 0.010 530 -3100 -213.1996 0.010 530 -3200 -213.1945 0.010 530 +5888 -212.7273 0.010 3769 +5900 -212.7273 0.010 3769 +6000 -212.7263 0.010 3769 +6100 -212.7249 0.010 3769 +6200 -212.7248 0.010 3769 +6300 -212.7245 0.010 3769 Reached termination condition! -last topological improvement at gen 530 -Improvement over last 500 gen = 0.03033 +last topological improvement at gen 3769 +Improvement over last 500 gen = 0.04406 MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: 6 rates - AC = 2.795, AG = 5.882, AT = 0.224, CG = 5.586, CT = 3.607, GT = 1.000 + AC = 4.838, AG = 9.614, AT = 0.397, CG = 9.747, CT = 6.243, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.2245 0.2962 0.1812 0.2981 + (ACGT) 0.2212 0.2915 0.1818 0.3056 Rate Heterogeneity Model: no rate heterogeneity NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - No branches were short enough to be collapsed. + 1 branches were collapsed. Saving site likelihoods to file ch.n.sitelikes.log ... @@ -14293,15 +14341,15 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -213.1945 +Replicate 1 : -212.7245 Parameter estimates: r(AC) r(AG) r(AT) r(CG) r(CT) r(GT) pi(A) pi(C) pi(G) pi(T) -rep 1: 2.795 5.882 0.2243 5.586 3.607 1 0.224 0.296 0.181 0.298 +rep 1: 4.838 9.614 0.397 9.747 6.243 1 0.221 0.291 0.182 0.306 Treelengths: TL -rep 1: 1.732 +rep 1: 1.730 Saving final tree from best search rep (#1) to ch.n.best.tre Inferring internal state probabilities on best tree... saving to file ch.n.internalstates.log @@ -14434,6 +14482,8 @@ 1600 -211.2007 0.010 1502 1800 -211.0869 0.010 1502 2000 -210.9557 0.010 1990 +2200 -210.8887 0.010 1990 +2400 -210.8702 0.010 1990 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -14521,14 +14571,9 @@ STARTING RUN Restarting from checkpoint... - generation 2063, seed 769068524, best lnL -210.940 + generation 2520, seed 720315951, best lnL -210.853 gen current_lnL precision last_tree_imp -2063 -210.9396 0.010 1990 -2100 -210.8915 0.010 1990 -2200 -210.8887 0.010 1990 -2300 -210.8736 0.010 1990 -2400 -210.8702 0.010 1990 -2500 -210.8529 0.010 1990 +2520 -210.8528 0.010 1990 2600 -210.7896 0.010 1990 2700 -210.7891 0.010 1990 2800 -210.7613 0.010 1990 @@ -14908,9 +14953,9 @@ Subset 3: Random seed for bootstrap reweighting: 1903425807 Restarting from checkpoint... -Bootstrap rep 1 (of 1) generation 81, seed 1912233251, best lnL -13185.207 +Bootstrap rep 1 (of 1) generation 86, seed 2143811610, best lnL -13185.143 gen current_lnL precision last_tree_imp -81 -13185.2068 0.500 1 +86 -13185.1432 0.500 1 100 -13185.0341 0.500 1 NOTE: ****Specified time limit (1 seconds) reached... @@ -14936,7 +14981,7 @@ Number of states = 4 (nucleotide data) Nucleotide Relative Rate Matrix: User specified matrix type: ( 0 1 2 1 0 3 ) - AC = 3.907, AG = 4.705, AT = 0.756, CG = 4.705, CT = 3.907, GT = 1.000 + AC = 3.907, AG = 4.751, AT = 0.756, CG = 4.751, CT = 3.907, GT = 1.000 Equilibrium State Frequencies: estimated (ACGT) 0.2477 0.1591 0.1965 0.3967 Rate Heterogeneity Model: @@ -14955,7 +15000,7 @@ User specified matrix type: ( 0 1 2 3 1 0 ) AC = 1.000, AG = 7.207, AT = 5.557, CG = 1.037, CT = 7.207, GT = 1.000 Equilibrium State Frequencies: estimated - (ACGT) 0.1648 0.3350 0.2990 0.2012 + (ACGT) 0.1658 0.3371 0.2946 0.2024 Rate Heterogeneity Model: 4 discrete gamma distributed rate categories, alpha param estimated 4.0686 @@ -14984,7 +15029,7 @@ Completed 1 replicate search(es) (of 1). Results: -Replicate 1 : -13184.9031 (TERMINATED PREMATURELY) +Replicate 1 : -13184.9131 (TERMINATED PREMATURELY) Parameter estimates: @@ -14994,11 +15039,11 @@ 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: 3.907 4.705 0.7563 4.705 3.907 1 0.248 0.159 0.197 0.397 0.403 +rep 1: 3.907 4.751 0.7563 4.751 3.907 1 0.248 0.159 0.197 0.397 0.403 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 7.207 5.557 1.037 7.207 1 0.165 0.335 0.299 0.201 4.069 0.010 +rep 1: 1 7.207 5.557 1.037 7.207 1 0.166 0.337 0.295 0.202 4.069 0.010 Treelengths and subset rate multipliers: TL R(1) R(2) R(3) @@ -15178,6 +15223,23 @@ 800 -467.7476 0.010 76 900 -467.7464 0.010 76 1000 -467.7420 0.010 76 +1100 -467.7366 0.010 76 +1200 -467.7323 0.010 76 +1300 -467.7309 0.010 76 +1400 -467.7300 0.010 76 +1500 -467.7294 0.010 76 +1600 -467.7287 0.010 76 +1700 -467.7245 0.010 76 +1800 -467.7232 0.010 76 +1900 -467.7232 0.010 76 +2000 -467.7227 0.010 76 +2100 -467.7221 0.010 76 +2200 -467.7211 0.010 76 +2300 -467.7209 0.010 76 +2400 -467.7201 0.010 76 +2500 -467.7198 0.010 76 +2600 -467.7198 0.010 76 +2700 -467.7190 0.010 76 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15303,39 +15365,154 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 1084, seed 1437212534, best lnL -467.740 +Search rep 1 (of 5) generation 2769, seed 1001429834, best lnL -467.719 gen current_lnL precision last_tree_imp -1084 -467.7404 0.010 76 -1100 -467.7366 0.010 76 -1200 -467.7323 0.010 76 -1300 -467.7309 0.010 76 -1400 -467.7300 0.010 76 -1500 -467.7294 0.010 76 -1600 -467.7287 0.010 76 -1700 -467.7245 0.010 76 -1800 -467.7232 0.010 76 -1900 -467.7232 0.010 76 -2000 -467.7227 0.010 76 -2100 -467.7221 0.010 76 -2200 -467.7211 0.010 76 +2769 -467.7185 0.010 76 +2800 -467.7182 0.010 76 +2900 -467.7178 0.010 76 +3000 -467.7177 0.010 76 +3100 -467.7174 0.010 76 +3200 -467.7172 0.010 76 +3300 -467.7172 0.010 76 +3400 -467.7171 0.010 76 +Reached termination condition! +last topological improvement at gen 76 +Improvement over last 500 gen = 0.00072 +Current score = -467.7171 +Performing final optimizations... +pass 1 : -467.7123 (branch= 0.0000 subset rates= 0.0049) +pass 2 : -467.6924 (branch= 0.0182 subset rates= 0.0017) +pass 3 : -467.6906 (branch= 0.0018 subset rates= 0.0000) +pass 4 : -467.6865 (branch= 0.0041 subset rates= 0.0000) +pass 5 : -467.6834 (branch= 0.0017 subset rates= 0.0014) +pass 6 : -467.6815 (branch= 0.0019 subset rates= 0.0000) +pass 7 : -467.6805 (branch= 0.0010 subset rates= 0.0000) +pass 8 : -467.6794 (branch= 0.0005 subset rates= 0.0007) +pass 9 : -467.6789 (branch= 0.0005 subset rates= 0.0000) +pass 10: -467.6786 (branch= 0.0003 subset rates= 0.0000) +pass 11: -467.6784 (branch= 0.0002 subset rates= 0.0000) +pass 12: -467.6784 (branch= 0.0001 subset rates= 0.0000) +pass 13: -467.6784 (branch= 0.0000 subset rates= 0.0000) +pass 14: -467.6783 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -467.6783 +Time used so far = 0 hours, 0 minutes and 7 seconds + +MODEL REPORT - Parameter values are FINAL +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.79 1.48 2.18 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (standard data) + Character change matrix: + One rate (symmetric one rate Mk model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=864977241 + +Initial ln Likelihood: -614.0831 +optimizing: starting branch lengths, subset rates... +pass 1:+ 127.392 (branch= 121.24 scale= 1.98 subset rates= 4.16) +pass 2:+ 15.987 (branch= 15.02 scale= 0.02 subset rates= 0.96) +pass 3:+ 2.694 (branch= 2.46 scale= 0.04 subset rates= 0.20) +pass 4:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 5:+ 0.039 (branch= 0.04 scale= 0.00 subset rates= 0.00) +pass 6:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -467.8366 +gen current_lnL precision last_tree_imp +0 -467.8366 0.010 0 +100 -467.8013 0.010 0 +200 -467.7834 0.010 0 +300 -467.7719 0.010 0 +400 -467.7465 0.010 0 +500 -467.7421 0.010 0 +600 -467.7393 0.010 0 +700 -467.7358 0.010 0 +800 -467.7328 0.010 0 +900 -467.7314 0.010 0 +1000 -467.7285 0.010 0 +1100 -467.7271 0.010 0 +1200 -467.7201 0.010 0 +1300 -467.7189 0.010 0 +1400 -467.7172 0.010 0 +1500 -467.7147 0.010 0 +1600 -467.7146 0.010 0 +1700 -467.7131 0.010 0 +1800 -467.7123 0.010 0 +1900 -467.7122 0.010 0 +2000 -467.7120 0.010 0 +2100 -467.7104 0.010 0 +2200 -467.7087 0.010 0 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -467.7211 +Current score = -467.7087 Performing final optimizations... -pass 1 : -467.7191 (branch= 0.0000 subset rates= 0.0019) -pass 2 : -467.7003 (branch= 0.0188 subset rates= 0.0000) -pass 3 : -467.6936 (branch= 0.0018 subset rates= 0.0049) -pass 4 : -467.6881 (branch= 0.0055 subset rates= 0.0000) -pass 5 : -467.6849 (branch= 0.0032 subset rates= 0.0000) -pass 6 : -467.6814 (branch= 0.0031 subset rates= 0.0005) -pass 7 : -467.6795 (branch= 0.0019 subset rates= 0.0000) -pass 8 : -467.6790 (branch= 0.0005 subset rates= 0.0000) -pass 9 : -467.6788 (branch= 0.0002 subset rates= 0.0000) -pass 10: -467.6785 (branch= 0.0001 subset rates= 0.0001) -pass 11: -467.6783 (branch= 0.0002 subset rates= 0.0000) -pass 12: -467.6783 (branch= 0.0000 subset rates= 0.0000) -pass 13: -467.6782 (branch= 0.0000 subset rates= 0.0000) -pass 14: -467.6782 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -467.7087 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -467.6904 (branch= 0.0183 subset rates= 0.0000) +pass 3 : -467.6880 (branch= 0.0024 subset rates= 0.0000) +pass 4 : -467.6848 (branch= 0.0032 subset rates= 0.0000) +pass 5 : -467.6822 (branch= 0.0026 subset rates= 0.0000) +pass 6 : -467.6800 (branch= 0.0022 subset rates= 0.0000) +pass 7 : -467.6795 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -467.6793 (branch= 0.0002 subset rates= 0.0000) +pass 9 : -467.6791 (branch= 0.0003 subset rates= 0.0000) +pass 10: -467.6789 (branch= 0.0002 subset rates= 0.0000) +pass 11: -467.6788 (branch= 0.0000 subset rates= 0.0000) +pass 12: -467.6786 (branch= 0.0000 subset rates= 0.0003) +pass 13: -467.6783 (branch= 0.0002 subset rates= 0.0000) +pass 14: -467.6783 (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 @@ -15370,7 +15547,7 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 1 (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!*** @@ -15378,9 +15555,13 @@ ####################################################### -Completed 1 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 : -467.6782 (best) (TERMINATED PREMATURELY) +Replicate 1 : -467.6783 +Replicate 2 : -467.6782 (best) (same topology as 1) (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15395,9 +15576,10 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.843 0.786 1.479 2.180 +rep 1: 3.842 0.787 1.476 2.177 +rep 2: 3.842 0.787 1.475 2.185 -Saving final tree from best search rep (#1) to ch.p.mk.ssr.best.tre +Saving final tree from best search rep (#2) to ch.p.mk.ssr.best.tre ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkO.ssr.conf @@ -15570,6 +15752,21 @@ 800 -477.2678 0.010 555 900 -477.2613 0.010 555 1000 -477.2592 0.010 555 +1100 -477.2583 0.010 555 +1200 -477.2566 0.010 555 +1300 -477.2538 0.010 555 +1400 -477.2535 0.010 555 +1500 -477.2523 0.010 555 +1600 -477.2498 0.010 555 +1700 -477.2480 0.010 555 +1800 -477.2471 0.010 555 +1900 -477.2449 0.010 555 +2000 -477.2435 0.010 555 +2100 -477.2427 0.010 555 +2200 -477.2409 0.010 555 +2300 -477.2408 0.010 555 +2400 -477.2396 0.010 555 +2500 -477.2391 0.010 555 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -15695,36 +15892,142 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 1005, seed 1354986070, best lnL -477.259 +Search rep 1 (of 5) generation 2593, seed 1330636286, best lnL -477.239 gen current_lnL precision last_tree_imp -1005 -477.2592 0.010 555 -1100 -477.2583 0.010 555 -1200 -477.2566 0.010 555 -1300 -477.2538 0.010 555 -1400 -477.2535 0.010 555 -1500 -477.2523 0.010 555 -1600 -477.2498 0.010 555 -1700 -477.2480 0.010 555 -1800 -477.2471 0.010 555 -1900 -477.2449 0.010 555 -2000 -477.2435 0.010 555 -NOTE: ****Specified time limit (5 seconds) reached... -Current score = -477.2428 +2593 -477.2388 0.010 555 +2600 -477.2388 0.010 555 +2700 -477.2384 0.010 555 +2800 -477.2381 0.010 555 +2900 -477.2380 0.010 555 +3000 -477.2379 0.010 555 +3100 -477.2379 0.010 555 +Reached termination condition! +last topological improvement at gen 555 +Improvement over last 500 gen = 0.00089 +Current score = -477.2379 Performing final optimizations... -pass 1 : -477.2404 (branch= 0.0000 subset rates= 0.0024) -pass 2 : -477.2250 (branch= 0.0154 subset rates= 0.0000) -pass 3 : -477.2203 (branch= 0.0039 subset rates= 0.0009) -pass 4 : -477.2161 (branch= 0.0026 subset rates= 0.0015) -pass 5 : -477.2148 (branch= 0.0011 subset rates= 0.0002) -pass 6 : -477.2138 (branch= 0.0009 subset rates= 0.0001) -pass 7 : -477.2128 (branch= 0.0010 subset rates= 0.0000) -pass 8 : -477.2124 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -477.2121 (branch= 0.0004 subset rates= 0.0000) -pass 10: -477.2120 (branch= 0.0001 subset rates= 0.0000) -pass 11: -477.2120 (branch= 0.0000 subset rates= 0.0000) -pass 12: -477.2119 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -477.2340 (branch= 0.0000 subset rates= 0.0039) +pass 2 : -477.2203 (branch= 0.0125 subset rates= 0.0013) +pass 3 : -477.2158 (branch= 0.0045 subset rates= 0.0000) +pass 4 : -477.2151 (branch= 0.0007 subset rates= 0.0000) +pass 5 : -477.2147 (branch= 0.0004 subset rates= 0.0000) +pass 6 : -477.2138 (branch= 0.0009 subset rates= 0.0000) +pass 7 : -477.2129 (branch= 0.0009 subset rates= 0.0000) +pass 8 : -477.2124 (branch= 0.0004 subset rates= 0.0001) +pass 9 : -477.2123 (branch= 0.0002 subset rates= 0.0000) +pass 10: -477.2120 (branch= 0.0002 subset rates= 0.0000) +pass 11: -477.2120 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.2120 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.2119 (branch= 0.0000 subset rates= 0.0000) +pass 14: -477.2119 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -477.2119 +Time used so far = 0 hours, 0 minutes and 7 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: + 0.64 1.91 2.62 +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 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=252102634 + +Initial ln Likelihood: -636.7211 +optimizing: starting branch lengths, subset rates... +pass 1:+ 139.100 (branch= 128.20 scale= 0.92 subset rates= 9.98) +pass 2:+ 13.649 (branch= 9.61 scale= 0.01 subset rates= 4.02) +pass 3:+ 4.086 (branch= 2.80 scale= 0.00 subset rates= 1.28) +pass 4:+ 1.602 (branch= 1.27 scale= 0.01 subset rates= 0.32) +pass 5:+ 0.321 (branch= 0.31 scale= 0.00 subset rates= 0.01) +pass 6:+ 0.086 (branch= 0.09 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -477.8776 +gen current_lnL precision last_tree_imp +0 -477.8776 0.010 0 +100 -477.8122 0.010 0 +200 -477.7411 0.010 130 +300 -477.7356 0.010 130 +400 -477.7278 0.010 130 +500 -477.6999 0.010 130 +600 -477.6940 0.010 130 +700 -477.6855 0.010 130 +800 -477.6803 0.010 130 +900 -477.6771 0.010 130 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -477.6715 +Performing final optimizations... +pass 1 : -477.6627 (branch= 0.0063 subset rates= 0.0024) +pass 2 : -477.6371 (branch= 0.0256 subset rates= 0.0000) +pass 3 : -477.6312 (branch= 0.0059 subset rates= 0.0000) +pass 4 : -477.6262 (branch= 0.0051 subset rates= 0.0000) +pass 5 : -477.6201 (branch= 0.0060 subset rates= 0.0000) +pass 6 : -477.6185 (branch= 0.0016 subset rates= 0.0000) +pass 7 : -477.6180 (branch= 0.0005 subset rates= 0.0001) +pass 8 : -477.6176 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -477.6174 (branch= 0.0001 subset rates= 0.0001) +pass 10: -477.6173 (branch= 0.0001 subset rates= 0.0000) +pass 11: -477.6172 (branch= 0.0001 subset rates= 0.0000) +pass 12: -477.6172 (branch= 0.0000 subset rates= 0.0000) +pass 13: -477.6169 (branch= 0.0000 subset rates= 0.0002) +pass 14: -477.6169 (branch= 0.0000 subset rates= 0.0000) +pass 15: -477.6169 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -477.6169 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -15753,11 +16056,11 @@ no rate heterogeneity Subset rate multipliers: - 0.64 1.91 2.62 + 0.63 1.90 2.74 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 8 branches were collapsed. ->>>Terminated Search rep 1 (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!*** @@ -15765,9 +16068,13 @@ ####################################################### -Completed 1 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 : -477.2119 (best) (TERMINATED PREMATURELY) +Replicate 1 : -477.2119 (best) +Replicate 2 : -477.6169 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -15782,7 +16089,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.672 0.642 1.909 2.619 +rep 1: 4.670 0.643 1.909 2.616 +rep 2: 4.890 0.634 1.903 2.744 Saving final tree from best search rep (#1) to ch.p.mkO.ssr.best.tre ####################################################### @@ -15961,6 +16269,9 @@ 800 -484.6300 0.010 630 900 -484.6226 0.010 630 1000 -484.6172 0.010 630 +1100 -484.6147 0.010 630 +1200 -484.6133 0.010 630 +1300 -484.6112 0.010 630 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16089,12 +16400,9 @@ Subset 3: Random seed for bootstrap reweighting: 585640194 Restarting from checkpoint... -Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 1059, seed 1336803846, best lnL -484.616 +Bootstrap rep 1 (of 1) Search rep 1 (of 5) generation 1304, seed 641898144, best lnL -484.611 gen current_lnL precision last_tree_imp -1059 -484.6163 0.010 630 -1100 -484.6147 0.010 630 -1200 -484.6133 0.010 630 -1300 -484.6112 0.010 630 +1304 -484.6112 0.010 630 1400 -484.6053 0.010 630 1500 -484.6017 0.010 630 1600 -484.5989 0.010 630 @@ -16104,26 +16412,41 @@ 2000 -484.5896 0.010 630 2100 -484.5884 0.010 630 2200 -484.5876 0.010 630 -NOTE: ****Specified time limit (5 seconds) reached... -Current score = -484.5874 +2300 -484.5871 0.010 630 +2400 -484.5867 0.010 630 +2500 -484.5850 0.010 630 +2600 -484.5848 0.010 630 +2700 -484.5843 0.010 630 +2800 -484.5843 0.010 630 +2900 -484.5836 0.010 630 +3000 -484.5832 0.010 630 +3100 -484.5829 0.010 630 +3200 -484.5826 0.010 630 +3300 -484.5825 0.010 630 +3400 -484.5825 0.010 630 +3500 -484.5823 0.010 630 +Reached termination condition! +last topological improvement at gen 630 +Improvement over last 500 gen = 0.00092 +Current score = -484.5823 Performing final optimizations... -pass 1 : -484.5788 (branch= 0.0086 subset rates= 0.0000) -pass 2 : -484.5572 (branch= 0.0216 subset rates= 0.0000) -pass 3 : -484.5530 (branch= 0.0042 subset rates= 0.0000) -pass 4 : -484.5489 (branch= 0.0037 subset rates= 0.0004) -pass 5 : -484.5463 (branch= 0.0026 subset rates= 0.0000) -pass 6 : -484.5446 (branch= 0.0017 subset rates= 0.0000) -pass 7 : -484.5432 (branch= 0.0014 subset rates= 0.0000) -pass 8 : -484.5431 (branch= 0.0001 subset rates= 0.0000) -pass 9 : -484.5429 (branch= 0.0002 subset rates= 0.0000) -pass 10: -484.5429 (branch= 0.0001 subset rates= 0.0000) -pass 11: -484.5428 (branch= 0.0001 subset rates= 0.0000) +pass 1 : -484.5737 (branch= 0.0084 subset rates= 0.0002) +pass 2 : -484.5520 (branch= 0.0217 subset rates= 0.0000) +pass 3 : -484.5480 (branch= 0.0040 subset rates= 0.0000) +pass 4 : -484.5463 (branch= 0.0017 subset rates= 0.0000) +pass 5 : -484.5443 (branch= 0.0019 subset rates= 0.0000) +pass 6 : -484.5441 (branch= 0.0003 subset rates= 0.0000) +pass 7 : -484.5436 (branch= 0.0005 subset rates= 0.0000) +pass 8 : -484.5431 (branch= 0.0004 subset rates= 0.0000) +pass 9 : -484.5430 (branch= 0.0002 subset rates= 0.0000) +pass 10: -484.5428 (branch= 0.0001 subset rates= 0.0000) +pass 11: -484.5428 (branch= 0.0000 subset rates= 0.0000) pass 12: -484.5428 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... Final score = -484.5428 -Time used so far = 0 hours, 0 minutes and 12 seconds +Time used so far = 0 hours, 0 minutes and 10 seconds -MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT +MODEL REPORT - Parameter values are FINAL Model 1 Number of states = 2 (standard data) Character change matrix: @@ -16153,7 +16476,75 @@ NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) 7 branches were collapsed. ->>>Terminated Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< +>>>Completed Bootstrap rep 1 (of 1) Search rep 1 (of 5)<<< + +>>>Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +Starting with seed=1505751468 + +Initial ln Likelihood: -709.4032 +optimizing: starting branch lengths, subset rates... +pass 1:+ 188.851 (branch= 178.18 scale= 1.58 subset rates= 9.09) +pass 2:+ 14.261 (branch= 10.15 scale= 0.01 subset rates= 4.10) +pass 3:+ 8.888 (branch= 7.63 scale= 0.01 subset rates= 1.24) +pass 4:+ 0.846 (branch= 0.75 scale= 0.00 subset rates= 0.09) +pass 5:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -496.5565 +gen current_lnL precision last_tree_imp +0 -496.5565 0.010 0 +100 -493.4088 0.010 45 +200 -493.0032 0.010 159 +300 -492.4979 0.010 267 +400 -486.8717 0.010 394 +NOTE: ****Specified time limit (5 seconds) reached... +Current score = -486.8682 +Performing final optimizations... +pass 1 : -486.7723 (branch= 0.0392 subset rates= 0.0566) +pass 2 : -486.7207 (branch= 0.0354 subset rates= 0.0163) +pass 3 : -486.6935 (branch= 0.0226 subset rates= 0.0046) +pass 4 : -486.6872 (branch= 0.0063 subset rates= 0.0000) +pass 5 : -486.6833 (branch= 0.0038 subset rates= 0.0000) +pass 6 : -486.6793 (branch= 0.0023 subset rates= 0.0018) +pass 7 : -486.6787 (branch= 0.0005 subset rates= 0.0001) +pass 8 : -486.6765 (branch= 0.0013 subset rates= 0.0008) +pass 9 : -486.6765 (branch= 0.0001 subset rates= 0.0000) +pass 10: -486.6764 (branch= 0.0001 subset rates= 0.0000) +pass 11: -486.6764 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -486.6764 +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) + 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: + 0.66 2.08 2.61 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 10 branches were collapsed. + +>>>Terminated Bootstrap rep 1 (of 1) Search rep 2 (of 5)<<< NOTE: ***Search was terminated before full auto-termination condition was reached! Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** @@ -16161,9 +16552,13 @@ ####################################################### -Completed 1 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 : -484.5428 (best) (TERMINATED PREMATURELY) +Replicate 1 : -484.5428 (best) +Replicate 2 : -486.6764 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16178,11 +16573,11 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 3.519 0.660 2.001 2.949 +rep 1: 3.519 0.661 1.998 2.951 +rep 2: 3.686 0.658 2.085 2.615 Saving tree from best search rep (#1) to bootstrap file ch.p.mkv.ssr.boot.tre -WARNING: Tree from prematurely terminated search saved to bootstrap file ####################################################### TREEFILES PASS Running checkpoint test ./check/p.mkvO.ssr.conf @@ -16354,6 +16749,22 @@ 600 -474.1362 0.010 560 700 -474.0417 0.010 653 800 -474.0258 0.010 653 +900 -474.0165 0.010 653 +1000 -474.0081 0.010 653 +1100 -474.0064 0.010 653 +1200 -474.0020 0.010 653 +1300 -474.0006 0.010 653 +1400 -473.9974 0.010 653 +1500 -473.9934 0.010 653 +1600 -473.9891 0.010 653 +1700 -473.9881 0.010 653 +1800 -473.9878 0.010 653 +1900 -473.9836 0.010 653 +2000 -473.9826 0.010 653 +2100 -473.9822 0.010 653 +2200 -473.9806 0.010 653 +2300 -473.9803 0.010 653 +2400 -473.9789 0.010 653 NOTE: ****Specified time limit (5 seconds) reached... NOTE: A CHECKPOINTED RUN (writecheckpoints = 1) WAS PREMATURELY @@ -16479,35 +16890,141 @@ STARTING RUN Restarting from checkpoint... -Search rep 1 (of 5) generation 805, seed 585523514, best lnL -474.026 +Search rep 1 (of 5) generation 2409, seed 1621963071, best lnL -473.979 gen current_lnL precision last_tree_imp -805 -474.0258 0.010 653 -900 -474.0165 0.010 653 -1000 -474.0081 0.010 653 -1100 -474.0064 0.010 653 -1200 -474.0020 0.010 653 -1300 -474.0006 0.010 653 -1400 -473.9974 0.010 653 -1500 -473.9934 0.010 653 -1600 -473.9891 0.010 653 +2409 -473.9789 0.010 653 +2500 -473.9788 0.010 653 +2600 -473.9779 0.010 653 +2700 -473.9775 0.010 653 +2800 -473.9765 0.010 653 +2900 -473.9763 0.010 653 +3000 -473.9762 0.010 653 +3100 -473.9760 0.010 653 +3200 -473.9760 0.010 653 +3300 -473.9755 0.010 653 +Reached termination condition! +last topological improvement at gen 653 +Improvement over last 500 gen = 0.00094 +Current score = -473.9755 +Performing final optimizations... +pass 1 : -473.9755 (branch= 0.0000 subset rates= 0.0000) +pass 2 : -473.9577 (branch= 0.0178 subset rates= 0.0000) +pass 3 : -473.9577 (branch= 0.0000 subset rates= 0.0000) +pass 4 : -473.9577 (branch= 0.0000 subset rates= 0.0000) +pass 5 : -473.9564 (branch= 0.0013 subset rates= 0.0000) +pass 6 : -473.9558 (branch= 0.0006 subset rates= 0.0000) +pass 7 : -473.9539 (branch= 0.0006 subset rates= 0.0013) +pass 8 : -473.9533 (branch= 0.0006 subset rates= 0.0000) +pass 9 : -473.9520 (branch= 0.0002 subset rates= 0.0011) +pass 10: -473.9519 (branch= 0.0002 subset rates= 0.0000) +pass 11: -473.9518 (branch= 0.0001 subset rates= 0.0000) +pass 12: -473.9509 (branch= 0.0000 subset rates= 0.0009) +pass 13: -473.9508 (branch= 0.0001 subset rates= 0.0000) +pass 14: -473.9508 (branch= 0.0000 subset rates= 0.0000) +Looking for minimum length branches... +Final score = -473.9508 +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 Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 0.59 2.07 2.80 +NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) + 8 branches were collapsed. + +>>>Completed Search rep 1 (of 5)<<< + +>>>Search rep 2 (of 5)<<< +Obtained starting tree 1 from Nexus +MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) +Model 1 + Number of states = 2 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.50, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 2 + Number of states = 3 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.33, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Model 3 + Number of states = 4 (ordered standard data) + Character change matrix: + One rate (ordered symmetric one rate Mkv model) + Equilibrium State Frequencies: equal (0.25, fixed) + Rate Heterogeneity Model: + no rate heterogeneity + +Subset rate multipliers: + 1.00 1.00 1.00 +Starting with seed=2125680066 + +Initial ln Likelihood: -649.8224 +optimizing: starting branch lengths, subset rates... +pass 1:+ 148.288 (branch= 136.88 scale= 0.96 subset rates= 10.45) +pass 2:+ 18.126 (branch= 13.41 scale= 0.03 subset rates= 4.69) +pass 3:+ 5.651 (branch= 3.93 scale= 0.00 subset rates= 1.72) +pass 4:+ 2.344 (branch= 1.67 scale= 0.00 subset rates= 0.67) +pass 5:+ 0.474 (branch= 0.43 scale= 0.01 subset rates= 0.03) +pass 6:+ 0.134 (branch= 0.13 scale= 0.00 subset rates= 0.00) +pass 7:+ 0.000 (branch= 0.00 scale= 0.00 subset rates= 0.00) +lnL after optimization: -474.8070 +gen current_lnL precision last_tree_imp +0 -474.8070 0.010 0 +100 -474.7912 0.010 0 +200 -474.7020 0.010 123 +300 -474.5641 0.010 272 +400 -474.5189 0.010 272 +500 -474.5074 0.010 272 NOTE: ****Specified time limit (5 seconds) reached... -Current score = -473.9885 +Current score = -474.5046 Performing final optimizations... -pass 1 : -473.9870 (branch= 0.0000 subset rates= 0.0014) -pass 2 : -473.9674 (branch= 0.0196 subset rates= 0.0000) -pass 3 : -473.9657 (branch= 0.0017 subset rates= 0.0000) -pass 4 : -473.9598 (branch= 0.0059 subset rates= 0.0000) -pass 5 : -473.9550 (branch= 0.0048 subset rates= 0.0000) -pass 6 : -473.9540 (branch= 0.0010 subset rates= 0.0000) -pass 7 : -473.9534 (branch= 0.0006 subset rates= 0.0000) -pass 8 : -473.9530 (branch= 0.0004 subset rates= 0.0000) -pass 9 : -473.9527 (branch= 0.0002 subset rates= 0.0000) -pass 10: -473.9527 (branch= 0.0001 subset rates= 0.0000) -pass 11: -473.9526 (branch= 0.0000 subset rates= 0.0000) -pass 12: -473.9526 (branch= 0.0000 subset rates= 0.0000) -pass 13: -473.9526 (branch= 0.0000 subset rates= 0.0000) +pass 1 : -474.4821 (branch= 0.0224 subset rates= 0.0000) +pass 2 : -474.4582 (branch= 0.0239 subset rates= 0.0000) +pass 3 : -474.4439 (branch= 0.0143 subset rates= 0.0000) +pass 4 : -474.4367 (branch= 0.0072 subset rates= 0.0000) +pass 5 : -474.4325 (branch= 0.0041 subset rates= 0.0000) +pass 6 : -474.4314 (branch= 0.0011 subset rates= 0.0000) +pass 7 : -474.4306 (branch= 0.0008 subset rates= 0.0000) +pass 8 : -474.4298 (branch= 0.0008 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: -474.4292 (branch= 0.0001 subset rates= 0.0000) +pass 12: -474.4291 (branch= 0.0000 subset rates= 0.0000) +pass 13: -474.4291 (branch= 0.0000 subset rates= 0.0000) +pass 14: -474.4291 (branch= 0.0000 subset rates= 0.0000) +pass 15: -474.4291 (branch= 0.0000 subset rates= 0.0000) Looking for minimum length branches... -Final score = -473.9526 +Final score = -474.4291 Time used so far = 0 hours, 0 minutes and 12 seconds MODEL REPORT - SEARCH TERMINATED AFTER REACHING TIME LIMIT @@ -16536,11 +17053,11 @@ no rate heterogeneity Subset rate multipliers: - 0.58 2.07 2.85 + 0.59 2.02 2.93 NOTE: Collapsing of minimum length branches was requested (collapsebranches = 1) - 8 branches were collapsed. + 7 branches were collapsed. ->>>Terminated Search rep 1 (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!*** @@ -16548,9 +17065,13 @@ ####################################################### -Completed 1 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 : -473.9526 (best) (TERMINATED PREMATURELY) +Replicate 1 : -473.9508 (best) +Replicate 2 : -474.4291 (TERMINATED PREMATURELY) Parameter estimates across search replicates: @@ -16565,7 +17086,8 @@ Treelengths and subset rate multipliers: TL R(1) R(2) R(3) -rep 1: 4.355 0.585 2.066 2.846 +rep 1: 4.349 0.588 2.067 2.799 +rep 2: 4.597 0.590 2.021 2.930 Saving final tree from best search rep (#1) to ch.p.mkvO.ssr.best.tre ####################################################### @@ -16586,7 +17108,7 @@ dh_testroot dh_prep dh_auto_install - make -j3 install DESTDIR=/build/garli-2.1/debian/tmp AM_UPDATE_INFO_DIR=no + make -j6 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' @@ -16637,23 +17159,25 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'garli' in '../garli_2.1-3_armhf.deb'. dpkg-deb: building package 'garli-examples' in '../garli-examples_2.1-3_all.deb'. +dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-3_armhf.deb'. dpkg-deb: building package 'garli-mpi' in '../garli-mpi_2.1-3_armhf.deb'. +dpkg-deb: building package 'garli' in '../garli_2.1-3_armhf.deb'. dpkg-deb: building package 'garli-dbgsym' in '../garli-dbgsym_2.1-3_armhf.deb'. -dpkg-deb: building package 'garli-mpi-dbgsym' in '../garli-mpi-dbgsym_2.1-3_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../garli_2.1-3_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/27629/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/27629/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/16347 and its subdirectories -I: Current time: Fri Jul 17 13:11:24 -12 2020 -I: pbuilder-time-stamp: 1595034684 +I: removing directory /srv/workspace/pbuilder/27629 and its subdirectories +I: Current time: Sat Jul 18 15:28:20 +14 2020 +I: pbuilder-time-stamp: 1595035700