Diff of the two buildlogs: -- --- b1/build.log 2023-05-19 19:48:45.988581868 +0000 +++ b2/build.log 2023-05-19 20:14:07.921703733 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 19 07:32:24 -12 2023 -I: pbuilder-time-stamp: 1684524744 +I: Current time: Fri Jun 21 16:11:50 +14 2024 +I: pbuilder-time-stamp: 1718935910 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./libbpp-phyl_2.4.1.orig.tar.gz] I: copying [./libbpp-phyl_2.4.1-8.debian.tar.xz] I: Extracting source -gpgv: Signature made Wed Nov 30 05:58:43 2022 -12 +gpgv: Signature made Thu Dec 1 07:58:43 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -29,135 +29,167 @@ dpkg-source: info: applying remove_test_likelihood_nh.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/2862742/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 21 16:12 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.15(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='884782b3c007448d92df0a2a61cd14ec' - 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='2862742' - PS1='# ' - PS2='> ' + INVOCATION_ID=03329c75959f45aca31f4c10c2dde2fb + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=4148063 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFF5woZ7/pbuilderrc_iTzC --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFF5woZ7/b1 --logfile b1/build.log libbpp-phyl_2.4.1-8.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.oFF5woZ7/pbuilderrc_RpoN --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.oFF5woZ7/b2 --logfile b2/build.log --extrapackages usrmerge libbpp-phyl_2.4.1-8.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos11-amd64 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Apr 23 09:23 bash - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bunzip2 - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzcat - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Sep 18 2022 bzdiff - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Sep 18 2022 bzgrep - -rwxr-xr-x 3 root root 39224 Sep 18 2022 bzip2 - -rwxr-xr-x 1 root root 14568 Sep 18 2022 bzip2recover - lrwxrwxrwx 1 root root 6 Sep 18 2022 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Sep 18 2022 bzmore - -rwxr-xr-x 1 root root 44016 Sep 20 2022 cat - -rwxr-xr-x 1 root root 68656 Sep 20 2022 chgrp - -rwxr-xr-x 1 root root 64496 Sep 20 2022 chmod - -rwxr-xr-x 1 root root 72752 Sep 20 2022 chown - -rwxr-xr-x 1 root root 151152 Sep 20 2022 cp - -rwxr-xr-x 1 root root 125640 Jan 5 01:20 dash - -rwxr-xr-x 1 root root 121904 Sep 20 2022 date - -rwxr-xr-x 1 root root 89240 Sep 20 2022 dd - -rwxr-xr-x 1 root root 102200 Sep 20 2022 df - -rwxr-xr-x 1 root root 151344 Sep 20 2022 dir - -rwxr-xr-x 1 root root 88656 Mar 22 22:02 dmesg - lrwxrwxrwx 1 root root 8 Dec 19 01:33 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Dec 19 01:33 domainname -> hostname - -rwxr-xr-x 1 root root 43856 Sep 20 2022 echo - -rwxr-xr-x 1 root root 41 Jan 24 02:43 egrep - -rwxr-xr-x 1 root root 35664 Sep 20 2022 false - -rwxr-xr-x 1 root root 41 Jan 24 02:43 fgrep - -rwxr-xr-x 1 root root 85600 Mar 22 22:02 findmnt - -rwsr-xr-x 1 root root 35128 Mar 22 20:35 fusermount - -rwxr-xr-x 1 root root 203152 Jan 24 02:43 grep - -rwxr-xr-x 2 root root 2346 Apr 9 2022 gunzip - -rwxr-xr-x 1 root root 6447 Apr 9 2022 gzexe - -rwxr-xr-x 1 root root 98136 Apr 9 2022 gzip - -rwxr-xr-x 1 root root 22680 Dec 19 01:33 hostname - -rwxr-xr-x 1 root root 72824 Sep 20 2022 ln - -rwxr-xr-x 1 root root 53024 Mar 23 00:40 login - -rwxr-xr-x 1 root root 151344 Sep 20 2022 ls - -rwxr-xr-x 1 root root 207168 Mar 22 22:02 lsblk - -rwxr-xr-x 1 root root 97552 Sep 20 2022 mkdir - -rwxr-xr-x 1 root root 72912 Sep 20 2022 mknod - -rwxr-xr-x 1 root root 43952 Sep 20 2022 mktemp - -rwxr-xr-x 1 root root 59712 Mar 22 22:02 more - -rwsr-xr-x 1 root root 59704 Mar 22 22:02 mount - -rwxr-xr-x 1 root root 18744 Mar 22 22:02 mountpoint - -rwxr-xr-x 1 root root 142968 Sep 20 2022 mv - lrwxrwxrwx 1 root root 8 Dec 19 01:33 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 2 18:25 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 43952 Sep 20 2022 pwd - lrwxrwxrwx 1 root root 4 Apr 23 09:23 rbash -> bash - -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink - -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm - -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Nov 2 2022 run-parts - -rwxr-xr-x 1 root root 126424 Jan 5 07:55 sed - lrwxrwxrwx 1 root root 4 Jan 5 01:20 sh -> dash - -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep - -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty - -rwsr-xr-x 1 root root 72000 Mar 22 22:02 su - -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync - -rwxr-xr-x 1 root root 531984 Apr 6 02:25 tar - -rwxr-xr-x 1 root root 14520 Nov 2 2022 tempfile - -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch - -rwxr-xr-x 1 root root 35664 Sep 20 2022 true - -rwxr-xr-x 1 root root 14568 Mar 22 20:35 ulockmgr_server - -rwsr-xr-x 1 root root 35128 Mar 22 22:02 umount - -rwxr-xr-x 1 root root 43888 Sep 20 2022 uname - -rwxr-xr-x 2 root root 2346 Apr 9 2022 uncompress - -rwxr-xr-x 1 root root 151344 Sep 20 2022 vdir - -rwxr-xr-x 1 root root 72024 Mar 22 22:02 wdctl - lrwxrwxrwx 1 root root 8 Dec 19 01:33 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Apr 9 2022 zcat - -rwxr-xr-x 1 root root 1678 Apr 9 2022 zcmp - -rwxr-xr-x 1 root root 6460 Apr 9 2022 zdiff - -rwxr-xr-x 1 root root 29 Apr 9 2022 zegrep - -rwxr-xr-x 1 root root 29 Apr 9 2022 zfgrep - -rwxr-xr-x 1 root root 2081 Apr 9 2022 zforce - -rwxr-xr-x 1 root root 8103 Apr 9 2022 zgrep - -rwxr-xr-x 1 root root 2206 Apr 9 2022 zless - -rwxr-xr-x 1 root root 1842 Apr 9 2022 zmore - -rwxr-xr-x 1 root root 4577 Apr 9 2022 znew -I: user script /srv/workspace/pbuilder/2862742/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Apr 24 2023 bash + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep + -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 + -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover + lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore + -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat + -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp + -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod + -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown + -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp + -rwxr-xr-x 1 root root 125640 Jan 6 2023 dash + -rwxr-xr-x 1 root root 121904 Sep 21 2022 date + -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd + -rwxr-xr-x 1 root root 102200 Sep 21 2022 df + -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir + -rwxr-xr-x 1 root root 88656 Mar 24 2023 dmesg + lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname + -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo + -rwxr-xr-x 1 root root 41 Jan 25 2023 egrep + -rwxr-xr-x 1 root root 35664 Sep 21 2022 false + -rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep + -rwxr-xr-x 1 root root 85600 Mar 24 2023 findmnt + -rwsr-xr-x 1 root root 35128 Mar 23 2023 fusermount + -rwxr-xr-x 1 root root 203152 Jan 25 2023 grep + -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip + -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe + -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip + -rwxr-xr-x 1 root root 22680 Dec 20 2022 hostname + -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln + -rwxr-xr-x 1 root root 53024 Mar 24 2023 login + -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls + -rwxr-xr-x 1 root root 207168 Mar 24 2023 lsblk + -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir + -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod + -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp + -rwxr-xr-x 1 root root 59712 Mar 24 2023 more + -rwsr-xr-x 1 root root 59704 Mar 24 2023 mount + -rwxr-xr-x 1 root root 18744 Mar 24 2023 mountpoint + -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv + lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd + lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash + -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink + -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm + -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir + -rwxr-xr-x 1 root root 27560 Nov 3 2022 run-parts + -rwxr-xr-x 1 root root 126424 Jan 6 2023 sed + lrwxrwxrwx 1 root root 9 Jun 21 16:12 sh -> /bin/bash + -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep + -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty + -rwsr-xr-x 1 root root 72000 Mar 24 2023 su + -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync + -rwxr-xr-x 1 root root 531984 Apr 7 2023 tar + -rwxr-xr-x 1 root root 14520 Nov 3 2022 tempfile + -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch + -rwxr-xr-x 1 root root 35664 Sep 21 2022 true + -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server + -rwsr-xr-x 1 root root 35128 Mar 24 2023 umount + -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname + -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress + -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir + -rwxr-xr-x 1 root root 72024 Mar 24 2023 wdctl + lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat + -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp + -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff + -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep + -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep + -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce + -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep + -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless + -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore + -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 51 http://deb.debian.org/debian bookworm/main amd64 libbpp-core-dev amd64 2.4.1-9 [944 kB] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libbpp-seq12 amd64 2.4.1-9 [497 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libbpp-seq-dev amd64 2.4.1-9 [728 kB] -Fetched 35.1 MB in 2s (19.8 MB/s) +Fetched 35.1 MB in 1s (47.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) @@ -478,8 +510,19 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/libbpp-phyl-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-phyl_2.4.1-8_source.changes +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +removed '/etc/unsupported-skip-usrmerge-conversion' +The system has been successfully converted. +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/libbpp-phyl-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbpp-phyl_2.4.1-8_source.changes dpkg-buildpackage: info: source package libbpp-phyl dpkg-buildpackage: info: source version 2.4.1-8 dpkg-buildpackage: info: source distribution unstable @@ -530,7 +573,7 @@ -- Build files have been written to: /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu dh_auto_build - cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/libbpp-phyl-2.4.1 -B/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks @@ -547,685 +590,682 @@ make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/bpp-phyl-shared.dir/build.make src/CMakeFiles/bpp-phyl-shared.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o [ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionList.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/BipartitionList.cpp [ 1%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/BipartitionTools.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/App/PhylogeneticsApplicationTools.cpp.o -cd 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object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Distance/NeighborJoining.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Distance/NeighborJoining.cpp [ 5%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Graphics/CladogramPlot.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o +[ 21%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp +[ 22%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && 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src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp -[ 23%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp [ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PairedSiteLikelihoods.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp +[ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/DRTreeLikelihoodTools.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat 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/build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp [ 24%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_phyl_shared_EXPORTS -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MT src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -MF CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o.d -o CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/MarginalAncestralStateReconstruction.cpp -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/PseudoNewtonOptimizer.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 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CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RASTools.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RASTools.cpp -[ 25%] Building CXX object src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT src/CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -MF CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o.d -o CMakeFiles/bpp-phyl-static.dir/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp.o -c /build/libbpp-phyl-2.4.1/src/Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-phyl-shared.dir/Bpp/Phyl/Likelihood/NNIHomogeneousTreeLikelihood.cpp.o cd 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test/CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -MF CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o.d -o CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_detailed_simulations.cpp -make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build -make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 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CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping.cpp make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_simulations.dir/DependInfo.cmake --color= +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_parsimony.dir/DependInfo.cmake --color= +make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/depend make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build +make -f test/CMakeFiles/test_nhx.dir/build.make test/CMakeFiles/test_nhx.dir/build +[ 94%] Building CXX object test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_getpath.dir/DependInfo.cmake --color= +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_mapping.dir/test_mapping.cpp.o -MF CMakeFiles/test_mapping.dir/test_mapping.cpp.o.d -o CMakeFiles/test_mapping.dir/test_mapping.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping.cpp +make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend +make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp [ 94%] Building CXX object test/CMakeFiles/test_models.dir/test_models.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_models.dir/test_models.cpp.o -MF CMakeFiles/test_models.dir/test_models.cpp.o.d -o CMakeFiles/test_models.dir/test_models.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_models.cpp +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 94%] Building CXX object test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -make -f test/CMakeFiles/test_tree_rootat.dir/build.make test/CMakeFiles/test_tree_rootat.dir/depend -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -MF CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o.d -o CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_mapping_codon.cpp -[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_nhx.cpp +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make -f test/CMakeFiles/test_parsimony.dir/build.make test/CMakeFiles/test_parsimony.dir/build make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/libbpp-phyl-2.4.1 /build/libbpp-phyl-2.4.1/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_tree_rootat.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_simulations.dir/build.make test/CMakeFiles/test_simulations.dir/build +[ 94%] Building CXX object test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree.dir/build.make test/CMakeFiles/test_tree.dir/build -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 94%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_nhx.dir/test_nhx.cpp.o -MF CMakeFiles/test_nhx.dir/test_nhx.cpp.o.d -o CMakeFiles/test_nhx.dir/test_nhx.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_nhx.cpp make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_tree_getpath.dir/build.make test/CMakeFiles/test_tree_getpath.dir/build -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o 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test/CMakeFiles/test_tree.dir/test_tree.cpp.o +[ 95%] Building CXX object test/CMakeFiles/test_tree.dir/test_tree.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree.dir/test_tree.cpp.o -MF CMakeFiles/test_tree.dir/test_tree.cpp.o.d -o CMakeFiles/test_tree.dir/test_tree.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree.cpp -[ 95%] Building CXX object test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o make[3]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_simulations.dir/test_simulations.cpp.o -MF CMakeFiles/test_simulations.dir/test_simulations.cpp.o.d -o CMakeFiles/test_simulations.dir/test_simulations.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_simulations.cpp [ 96%] Building CXX object test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o +[ 96%] Building CXX object test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -MF CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o.d -o CMakeFiles/test_tree_getpath.dir/test_tree_getpath.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree_getpath.cpp +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -MF CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o.d -o CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_parsimony.cpp [ 96%] Building CXX object test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/c++ -I/build/libbpp-phyl-2.4.1/src -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -MD -MT test/CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -MF CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o.d -o CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -c /build/libbpp-phyl-2.4.1/test/test_tree_rootat.cpp [ 96%] Linking CXX executable test_tree_getpath @@ -1343,26 +1383,29 @@ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_nhx.dir/test_nhx.cpp.o -o test_nhx -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 97%] Built target test_nhx +[ 97%] Linking CXX executable test_models +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[ 97%] Built target test_models +/usr/bin/ranlib libbpp-phyl.a [ 98%] Linking CXX executable test_tree_rootat cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree_rootat.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree_rootat.dir/test_tree_rootat.cpp.o -o test_tree_rootat -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +[ 98%] Linking CXX executable test_parsimony +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_tree_rootat -[ 98%] Linking CXX executable test_models -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_models.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_models.dir/test_models.cpp.o -o test_models -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 98%] Built target test_models +[ 98%] Built target test_parsimony [ 98%] Linking CXX executable test_tree cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_tree.dir/test_tree.cpp.o -o test_tree -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 98%] Built target test_tree -[ 98%] Linking CXX executable test_parsimony -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parsimony.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_parsimony.dir/test_parsimony.cpp.o -o test_parsimony -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 98%] Built target test_parsimony +[ 98%] Built target bpp-phyl-static [ 99%] Linking CXX executable test_likelihood_clock cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood_clock.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood_clock.dir/test_likelihood_clock.cpp.o -o test_likelihood_clock -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 @@ -1371,27 +1414,27 @@ [ 99%] Linking CXX executable test_likelihood cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_likelihood.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_likelihood.dir/test_likelihood.cpp.o -o test_likelihood -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[ 99%] Built target test_likelihood [ 99%] Linking CXX executable test_detailed_simulations cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_detailed_simulations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_detailed_simulations.dir/test_detailed_simulations.cpp.o -o test_detailed_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[ 99%] Built target test_likelihood -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_detailed_simulations +[ 99%] Linking CXX executable test_bowker +cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 [100%] Linking CXX executable test_mapping_codon cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping_codon.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_mapping_codon.dir/test_mapping_codon.cpp.o -o test_mapping_codon -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' +[100%] Built target test_bowker +make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_mapping_codon -[100%] Linking CXX executable test_bowker -cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 [100%] Linking CXX executable test_simulations cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simulations.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/libbpp-phyl-2.4.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/test_simulations.dir/test_simulations.cpp.o -o test_simulations -Wl,-rpath,/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-phyl.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' -[100%] Built target test_bowker -make[3]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_simulations [100%] Linking CXX executable test_mapping cd /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mapping.dir/link.txt --verbose=1 @@ -1402,10 +1445,10 @@ /usr/bin/cmake -E cmake_progress_start /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' dh_auto_test - cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15 + cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16 make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j15 +/usr/bin/ctest --force-new-ctest-process --verbose -j16 UpdateCTestConfiguration from :/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl @@ -1495,11 +1538,54 @@ 13: Test command: /build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu/test/test_tree_rootat 13: Working Directory: /build/libbpp-phyl-2.4.1/test 13: Test timeout computed to be: 60000 -1: / 1 - 2 \ 3 nodes loaded. -1: ..:: Testing with homogeneous model ::.. 2: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 2: 4 +4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +5: 4x4 +5: [ +5: [-1.37306, 0.362694, 0.906736, 0.103627] +5: [0.103627, -0.984456, 0.362694, 0.518135] +5: [0.259067, 0.362694, -0.777202, 0.15544] +5: [0.0518135, 0.906736, 0.272021, -1.23057] +5: ] +6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. 3: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +1: / 1 - 2 \ 3 nodes loaded. +1: ..:: Testing with homogeneous model ::.. + 1/13 Test #8: test_nhx ......................... Passed 0.08 sec +12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +12: Id node1 0 +12: Id node2 1 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 1 +12: Id node1 0 +12: Id node3 2 +12: Ids of path: +12: 0 +12: 4 +12: 3 +12: 2 +9: Initializing data structure............: Done. +9: Number of distinct sites...............: 9 +9: Parsimony score: 9 +10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. +10: Theta0 set to 0.0942954 +10: Theta1 set to 0.498751 +10: Theta2 set to 0.318075 +10: Theta3 set to 0.675708 +10: Theta4 set to 0.0811184 +10: Fast check: +4: Test model.............................: T92 +4: 94.395699097704181213 +4: * initial likelihood...................: 94.3957 +4: Log-likelihood after adding clock......: 94.3957 +13: Total length...........................: 97.6347 3: Testing Single Tree Traversal likelihood class... 3: Initializing data structure............: Done. 3: Number of distinct sites...............: 12 @@ -1516,6 +1602,28 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 + 2/13 Test #9: test_parsimony ................... Passed 0.17 sec + 3/13 Test #12: test_tree_getpath ................ Passed 0.14 sec + 4/13 Test #7: test_models ...................... Passed 0.21 sec +4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 +4: +4: 71.26579958637299228 +4: * likelihood after full optimization...: 71.2658 +4: Name: Value: Constraint: +4: _________________________________________________ +4: BrLen0 0.143684 [ 1e-06; 10000] +4: BrLen1 0.143684 [ 1e-06; 10000] +4: BrLen2 0.031698 [ 1e-06; 10000] +4: BrLen3 0.175382 [ 1e-06; 10000] +4: BrLen4 0.272930 [ 1e-06; 10000] +4: BrLen5 0.448312 [ 1e-06; 10000] +4: T92.kappa 0.996464 ]0; +inf[ +4: T92.theta 0.579955 ]1e-06; 0.999999[ +4: Initializing data structure............: Done. +4: Number of distinct sites...............: 14 +4: Test model.............................: T92 +4: 92.32951163315719611546 +4: * initial likelihood...................: 92.3295 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215015147885 @@ -1536,69 +1644,6 @@ 3: Done. 3: Tree scaled by.........................: 8.31477 3: * likelihood after tree scale..........: 71.6905 -4: / 1 - 2 \ 3 - 4 / 5 - 6 \ 7 nodes loaded. -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 94.395699097704181213 -4: * initial likelihood...................: 94.3957 -4: Log-likelihood after adding clock......: 94.3957 -4: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 -4: -4: 71.26579958637299228 -4: * likelihood after full optimization...: 71.2658 -4: Name: Value: Constraint: -4: _________________________________________________ -4: BrLen0 0.143684 [ 1e-06; 10000] -4: BrLen1 0.143684 [ 1e-06; 10000] -4: BrLen2 0.031698 [ 1e-06; 10000] -4: BrLen3 0.175382 [ 1e-06; 10000] -4: BrLen4 0.272930 [ 1e-06; 10000] -4: BrLen5 0.448312 [ 1e-06; 10000] -4: T92.kappa 0.996464 ]0; +inf[ -4: T92.theta 0.579955 ]1e-06; 0.999999[ -4: Initializing data structure............: Done. -4: Number of distinct sites...............: 14 -4: Test model.............................: T92 -4: 92.32951163315719611546 -4: * initial likelihood...................: 92.3295 -5: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -5: 4x4 -5: [ -5: [-1.37306, 0.362694, 0.906736, 0.103627] -5: [0.103627, -0.984456, 0.362694, 0.518135] -5: [0.259067, 0.362694, -0.777202, 0.15544] -5: [0.0518135, 0.906736, 0.272021, -1.23057] -5: ] -6: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -9: Initializing data structure............: Done. -9: Number of distinct sites...............: 9 -9: Parsimony score: 9 -10: / 1 - 2 \ 3 - 4 / 5 - 6 nodes loaded. -10: Theta0 set to 0.0461786 -10: Theta1 set to 0.670565 -10: Theta2 set to 0.491673 -10: Theta3 set to 0.431136 -10: Theta4 set to 0.736677 -10: Fast check: - 1/13 Test #8: test_nhx ......................... Passed 0.07 sec - 2/13 Test #9: test_parsimony ................... Passed 0.07 sec -12: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -12: Id node1 0 -12: Id node2 1 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 1 -12: Id node1 0 -12: Id node3 2 -12: Ids of path: -12: 0 -12: 4 -12: 3 -12: 2 - 3/13 Test #12: test_tree_getpath ................ Passed 0.04 sec 4: Optimizing... / 1 Optimizing... \ 15 Optimizing... - 22 Optimizing... / 29 Optimizing... / 37 Optimizing... / 45 Optimizing... - 52 Optimizing... \ 59 Optimizing... \ 67 Optimizing... \ 75 Optimizing... / 81 Optimizing... - 88 Optimizing... \ 95 Optimizing... \ 103 Optimizing... - 110 Optimizing... - 116 Optimizing... - 124 Optimizing... \ 131 Optimizing... \ 139 Optimizing... \ 147 4: 4: 71.26579406919438497425 @@ -1610,8 +1655,7 @@ 4: HeightP2 0.819072 [ 0; 1] 4: T92.kappa 0.996398 ]0; +inf[ 4: T92.theta 0.579960 ]1e-06; 0.999999[ - 4/13 Test #4: test_likelihood_clock ............ Passed 0.14 sec -13: Total length...........................: 96.8519 + 5/13 Test #4: test_likelihood_clock ............ Passed 0.31 sec 3: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 3: 3: 65.72293577215069149133 @@ -1625,15 +1669,14 @@ 3: BrLen2 3.41183634475365238359 3.41183634475364838679 3: BrLen3 -187.23500312051925220658 -187.23500312051925220658 3: BrLen4 -56.02595035016005198258 -56.02595035016005908801 - 5/13 Test #3: test_likelihood .................. Passed 0.20 sec - 6/13 Test #7: test_models ...................... Passed 0.15 sec - 7/13 Test #13: test_tree_rootat ................. Passed 0.36 sec + 6/13 Test #3: test_likelihood .................. Passed 0.39 sec + 7/13 Test #13: test_tree_rootat ................. Passed 0.35 sec 10: Initializing data structure............: Done. -10: Number of distinct sites...............: 185 +10: Number of distinct sites...............: 179 5: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 78% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 5: Initializing data structure............: Done. -5: Number of distinct sites...............: 80 -5: 77619.6 +5: Number of distinct sites...............: 75 +5: 76987.2 5: Analytical (Laplace) total count: 5: 4x4 5: [ @@ -1642,57 +1685,57 @@ 5: [1.00009, 1.00032, 4.08766e-07, 1.00069] 5: [1.00159, 1.00007, 1.00069, 5.17576e-07] 5: ] -2: Br0 BrLen = 0.001 counts = 0.00098 +5: Compute joint node-pairs likelihood....: +5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. +5: Simple total count: +5: 4x4 +5: [ +5: [0, 1, 1, 1] +5: [1, 0, 1, 1] +5: [1, 1, 0, 1] +5: [1, 1, 1, 0] +5: ] +2: Br0 BrLen = 0.001 counts = 0.00115 2: 4x4 2: [ -2: [0, 2e-05, 5e-05, 0] -2: [4e-05, 0, 0.00014, 0.00017] -2: [0.00011, 0.00018, 0, 0.0001] -2: [1e-05, 0.00012, 4e-05, 0] +2: [0, 3e-05, 0.0001, 1e-05] +2: [1e-05, 0, 0.0002, 0.00029] +2: [5e-05, 0.00015, 0, 7e-05] +2: [2e-05, 0.00018, 4e-05, 0] 2: ] -2: Br1 BrLen = 0.002 counts = 0.00202 +2: Br1 BrLen = 0.002 counts = 0.0021 2: 4x4 2: [ -2: [0, 8e-05, 0.00025, 1e-05] -2: [6e-05, 0, 0.0002, 0.00042] -2: [0.00016, 0.00022, 0, 0.0001] -2: [1e-05, 0.00035, 0.00016, 0] +2: [0, 8e-05, 0.00011, 2e-05] +2: [2e-05, 0, 0.00024, 0.00042] +2: [0.00016, 0.00035, 0, 0.00015] +2: [3e-05, 0.00042, 0.0001, 0] 2: ] -2: Br2 BrLen = 0.003 counts = 0.00305 +2: Br2 BrLen = 0.003 counts = 0.003 2: 4x4 2: [ -2: [0, 0.00016, 0.00029, 5e-05] -2: [9e-05, 0, 0.00032, 0.00054] -2: [0.0002, 0.00046, 0, 0.00012] -2: [4e-05, 0.00062, 0.00016, 0] +2: [0, 0.00019, 0.00026, 3e-05] +2: [8e-05, 0, 0.00034, 0.00049] +2: [0.00031, 0.00034, 0, 0.00017] +2: [3e-05, 0.00056, 0.0002, 0] 2: ] -2: Br3 BrLen = 0.01 counts = 0.00994 +2: Br3 BrLen = 0.01 counts = 0.01008 2: 4x4 2: [ -2: [0, 0.00029, 0.00093, 9e-05] -2: [0.00032, 0, 0.00134, 0.00166] -2: [0.00098, 0.0012, 0, 0.00052] -2: [0.00017, 0.00192, 0.00052, 0] +2: [0, 0.00043, 0.0009, 5e-05] +2: [0.0003, 0, 0.00127, 0.0018] +2: [0.00104, 0.00114, 0, 0.00059] +2: [9e-05, 0.00177, 0.0007, 0] 2: ] -2: Br4 BrLen = 0.1 counts = 0.10114 +2: Br4 BrLen = 0.1 counts = 0.09876 2: 4x4 2: [ -2: [0, 0.00376, 0.00914, 0.00116] -2: [0.00351, 0, 0.0126, 0.01762] -2: [0.00954, 0.01309, 0, 0.00546] -2: [0.00097, 0.01861, 0.00568, 0] +2: [0, 0.00356, 0.00941, 0.00098] +2: [0.00341, 0, 0.01207, 0.01726] +2: [0.00897, 0.01274, 0, 0.00512] +2: [0.00098, 0.01868, 0.00558, 0] 2: ] - 8/13 Test #2: test_detailed_simulations ........ Passed 1.23 sec -5: Compute joint node-pairs likelihood....: -5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -5: Simple total count: -5: 4x4 -5: [ -5: [0, 1, 1, 1] -5: [1, 0, 1, 1] -5: [1, 1, 0, 1] -5: [1, 1, 1, 0] -5: ] + 8/13 Test #2: test_detailed_simulations ........ Passed 2.47 sec 5: Compute joint node-pairs likelihood....: 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: Detailed count, type 1: @@ -1743,36 +1786,7 @@ 5: [6.26538e-09, 0.000129478, 5.67996e-12, 5.21646e-08] 5: [6.2614e-09, 1.03721e-05, 4.17684e-09, 1.62422e-12] 5: ] -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4); -11: -11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A,B),C); -11: -11: ((A:1,B:2):3,C:4):5; -11: -11: ((A:1,B:2)80:3,C:4):5; -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: N: BOOTSTRAP=80 -11: Node 3: -11: Node 4: -11: N: BOOTSTRAP=2 -11: ((A,B),C); -11: -11: Node 0: -11: Node 1: -11: Node 2: -11: B: ESS=aa -11: Node 3: -11: Node 4: -11: B: ESS=2 5: Compute joint node-pairs likelihood....: -11: Newick I/O ok. 5: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 5: checking saturation... 5: Total count, uniformization method for 0.001 @@ -1847,17 +1861,46 @@ 5: [0.277113, 0.364216, 0.278181, 0.312009] 5: ] 5: 6.25012 -5: A 0.001 60 58.6158 58.5733 58.5733 58.6158 58.6158 58.6158 58.6158 -5: B 0.002 110 109.916 109.76 109.76 109.916 109.916 109.916 109.916 -5: 0.008 428 429.591 427.117 427.117 429.591 429.591 429.591 429.591 -5: C 0.01 492 486.584 482.829 482.829 486.584 486.584 486.584 486.584 -5: D 0.02 1056 1048.17 1032.67 1032.67 1048.17 1048.17 1048.17 1048.17 -5: A 0.001 2.00235/2 2.00488/2 2.00488/2 1.04792/2 1.05366/2 1.05366/2 1.99841/2 1.99612/2 1.99612/2 0.660859/1 0.662435/1 0.662435/1 -5: B 0.002 9.26187/9 9.25872/9 9.25872/9 12.0462/13 12.0689/13 12.0689/13 0.750515/1 0.752484/1 0.752484/1 2.99963/3 3.00323/3 3.00323/3 -5: 0.008 13.754/13 13.8266/13 13.8266/13 41.0136/41 41.2899/41 41.2899/41 3.01378/3 3.01976/3 3.01976/3 15.567/16 15.6117/16 15.6117/16 -5: C 0.01 12.5934/13 12.7372/13 12.7372/13 44.119/49 44.5285/49 44.5285/49 6.00355/5 5.97032/5 5.97032/5 16.9406/17 17.0625/17 17.0625/17 -5: D 0.02 32.2198/33 32.8464/33 32.8464/33 93.9823/100 95.7967/100 95.7967/100 15.3023/16 15.0821/16 15.0821/16 45.1817/47 45.4942/47 45.4942/47 - 9/13 Test #5: test_mapping ..................... Passed 2.71 sec +5: A 0.001 57 54.3552 54.3171 54.3171 54.3552 54.3552 54.3552 54.3552 +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4); +11: +11: / 1 - 2 \ 3 - 4 / 5 nodes loaded. +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A,B),C); +11: +11: ((A:1,B:2):3,C:4):5; +11: +11: ((A:1,B:2)80:3,C:4):5; +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: N: BOOTSTRAP=80 +11: Node 3: +11: Node 4: +11: N: BOOTSTRAP=2 +11: ((A,B),C); +11: +11: Node 0: +11: Node 1: +11: Node 2: +11: B: ESS=aa +11: Node 3: +11: Node 4: +11: B: ESS=2 +11: Newick I/O ok. +5: B 0.002 107 107.972 107.818 107.818 107.972 107.972 107.972 107.972 +5: 0.008 372 382.572 380.17 380.17 382.572 382.572 382.572 382.572 +5: C 0.01 523 520.681 516.753 516.753 520.681 520.681 520.681 520.681 +5: D 0.02 958 959.334 944.462 944.462 959.334 959.334 959.334 959.334 +5: A 0.001 3.00349/3 3.00328/3 3.00328/3 4.02985/4 4.03428/4 4.03428/4 0.00061355/0 0.00170631/0 0.00170631/0 0.995743/1 0.996352/1 0.996352/1 +5: B 0.002 3.00552/3 3.00886/3 3.00886/3 5.01944/5 5.03594/5 5.03594/5 0.000142515/0 0.00288255/0 0.00288255/0 3.99956/4 4.00338/4 4.00338/4 +5: 0.008 9.39839/10 9.49298/10 9.49298/10 36.2471/35 36.5202/35 36.5202/35 5.00162/5 4.97659/5 4.97659/5 12.9303/13 12.9984/13 12.9984/13 +5: C 0.01 11.625/12 11.7997/12 11.7997/12 39.8362/40 40.2831/40 40.2831/40 9.00393/9 8.92896/9 8.92896/9 21.8716/21 21.941/21 21.941/21 +5: D 0.02 41.2338/42 41.6067/42 41.6067/42 88.2784/89 90.0433/89 90.0433/89 10.2516/11 10.1924/11 10.1924/11 42.3534/43 42.6111/43 42.6111/43 + 9/13 Test #5: test_mapping ..................... Passed 5.57 sec 11: Newick multiple I/O ok. 11: Testing parsing a directory... 11: Ok, reading on directory throws exception! @@ -1887,25 +1930,15 @@ 11: / 1 - 2 \ 3 nodes loaded. 11: ((A:1):2); 11: -10/13 Test #11: test_tree ........................ Passed 5.85 sec -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0389 0.0061 +10/13 Test #11: test_tree ........................ Passed 9.76 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0384 0.0054 1: ..:: Testing with homogeneous, non-stationary model ::.. -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 -10: -10: 0.0461786 0.0484808 -10: 0.670565 0.668054 -10: 0.491673 0.494837 -10: 0.431136 0.420023 -10: 0.736677 0.734908 -10: Detailed check: -10: Initializing data structure............: Done. -10: Number of distinct sites...............: 182 -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0375 0.0045 -1: ..:: Testing with non-homogeneous, non-stationary model ::.. 6: [ ] 0% [= ] 2% [== ] 5% [=== ] 7% [==== ] 10% [===== ] 13% [====== ] 15% [======= ] 18% [======== ] 21% [========= ] 23% [========== ] 26% [=========== ] 28% [============ ] 31% [============= ] 34% [============== ] 36% [=============== ] 39% [================ ] 42% [================= ] 44% [================== ] 47% [=================== ] 50% [==================== ] 52% [===================== ] 55% [====================== ] 57% [======================= ] 60% [======================== ] 63% [========================= ] 65% [========================== ] 68% [=========================== ] 71% [============================ ] 73% [============================= ] 76% [============================== ] 79% [=============================== ] 81% [================================ ] 84% [================================= ] 86% [================================== ] 89% [=================================== ] 92% [==================================== ] 94% [===================================== ] 97% [======================================] 100%Done. 6: Initializing data structure............: Done. -6: Number of distinct sites...............: 990 -6: 96173.3 +6: Number of distinct sites...............: 1016 +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0397 0.0056 +1: ..:: Testing with non-homogeneous, non-stationary model ::.. +6: 96501.6 6: Analytical total count: 6: 64x64 6: [ @@ -1975,14 +2008,6 @@ 6: [3.00169, 3.00145, 3.00139, 2.00023, 3.00149, 3.00181, 3.00139, 2.00023, 3.00136, 3.0016, 3.00152, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00144, 3.0014, 3.00135, 2.00023, 3.00092, 3.00161, 3.00111, 2.00023, 3.00164, 3.00171, 3.0018, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, 3.00157, 3.00128, 3.00143, 2.00023, 3.00155, 3.0017, 3.00158, 2.00023, 3.00136, 3.0013, 3.00154, 2.00023, 2.00023, 2.00023, 2.00023, 1.00012, -nan, 2.00015, -nan, 1.00012, 2.00015, 2.00023, 2.00019, 1.00012, -nan, 2.00019, 2.00015, 1.00012, 1.00012, 1.00012, 1.00012, 1.21058e-07] 6: ] 6: Compute joint node-pairs likelihood....: -10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 -10: -10: 0.0461786 0.0451522 -10: 0.670565 0.659962 -10: 0.491673 0.483537 -10: 0.431136 0.43762 -10: 0.736677 0.743536 -11/13 Test #10: test_simulations ................. Passed 14.83 sec 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. 6: Simple total count: 6: 64x64 @@ -2264,20 +2289,38 @@ 6: ] 6: Compute joint node-pairs likelihood....: 6: [ ] 0% [>>>>>>>>> ] 25% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 75% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% Done. -12/13 Test #6: test_mapping_codon ............... Passed 17.91 sec -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9366 0.8025 +11/13 Test #6: test_mapping_codon ............... Passed 27.46 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.9336 0.8048 1: ..:: Testing with non-homogeneous, stationary model ::.. -1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0382 0.0063 -13/13 Test #1: test_bowker ...................... Passed 23.48 sec +1: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0404 0.006 +12/13 Test #1: test_bowker ...................... Passed 37.77 sec +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 Optimizing... - 56 Optimizing... / 57 Optimizing... - 58 Optimizing... \ 59 Optimizing... - 60 Optimizing... / 61 Optimizing... - 62 Optimizing... \ 63 Optimizing... - 64 Optimizing... / 65 Optimizing... - 66 Optimizing... \ 67 Optimizing... - 68 Optimizing... / 69 Optimizing... - 70 Optimizing... \ 71 Optimizing... - 72 Optimizing... / 73 Optimizing... - 74 Optimizing... \ 75 Optimizing... - 76 Optimizing... / 77 Optimizing... - 78 Optimizing... \ 79 Optimizing... - 80 Optimizing... / 81 Optimizing... - 82 Optimizing... \ 83 Optimizing... - 84 Optimizing... / 85 Optimizing... - 86 Optimizing... \ 87 Optimizing... - 88 Optimizing... / 89 Optimizing... - 90 Optimizing... \ 91 Optimizing... - 92 Optimizing... / 93 Optimizing... - 94 Optimizing... \ 95 Optimizing... - 96 Optimizing... / 97 Optimizing... - 98 Optimizing... \ 99 Optimizing... - 100 Optimizing... / 101 Optimizing... - 102 Optimizing... \ 103 Optimizing... - 104 Optimizing... / 105 Optimizing... - 106 Optimizing... \ 107 Optimizing... - 108 Optimizing... / 109 Optimizing... - 110 Optimizing... \ 111 Optimizing... - 112 Optimizing... / 113 Optimizing... - 114 Optimizing... \ 115 Optimizing... - 116 Optimizing... / 117 Optimizing... - 118 Optimizing... \ 119 Optimizing... - 120 Optimizing... / 121 Optimizing... - 122 Optimizing... \ 123 Optimizing... - 124 Optimizing... / 125 Optimizing... - 126 Optimizing... \ 127 Optimizing... - 128 Optimizing... / 129 Optimizing... - 130 Optimizing... \ 131 Optimizing... - 132 Optimizing... / 133 Optimizing... - 134 Optimizing... \ 135 Optimizing... - 136 Optimizing... / 137 Optimizing... - 138 Optimizing... \ 139 Optimizing... - 140 Optimizing... / 141 Optimizing... - 142 Optimizing... \ 143 Optimizing... - 144 Optimizing... / 145 Optimizing... - 146 Optimizing... \ 147 Optimizing... - 148 Optimizing... / 149 Optimizing... - 150 Optimizing... \ 151 Optimizing... - 152 Optimizing... / 153 Optimizing... - 154 Optimizing... \ 155 Optimizing... - 156 Optimizing... / 157 Optimizing... - 158 Optimizing... \ 159 Optimizing... - 160 Optimizing... / 161 Optimizing... - 162 +10: +10: 0.0942954 0.0927283 +10: 0.498751 0.502655 +10: 0.318075 0.307743 +10: 0.675708 0.645233 +10: 0.0811184 0.0806645 +10: Detailed check: +10: Initializing data structure............: Done. +10: Number of distinct sites...............: 187 +10: Optimizing... / 1 Optimizing... - 2 Optimizing... \ 3 Optimizing... - 4 Optimizing... / 5 Optimizing... - 6 Optimizing... \ 7 Optimizing... - 8 Optimizing... / 9 Optimizing... - 10 Optimizing... \ 11 Optimizing... - 12 Optimizing... / 13 Optimizing... - 14 Optimizing... \ 15 Optimizing... - 16 Optimizing... / 17 Optimizing... - 18 Optimizing... \ 19 Optimizing... - 20 Optimizing... / 21 Optimizing... - 22 Optimizing... \ 23 Optimizing... - 24 Optimizing... / 25 Optimizing... - 26 Optimizing... \ 27 Optimizing... - 28 Optimizing... / 29 Optimizing... - 30 Optimizing... \ 31 Optimizing... - 32 Optimizing... / 33 Optimizing... - 34 Optimizing... \ 35 Optimizing... - 36 Optimizing... / 37 Optimizing... - 38 Optimizing... \ 39 Optimizing... - 40 Optimizing... / 41 Optimizing... - 42 Optimizing... \ 43 Optimizing... - 44 Optimizing... / 45 Optimizing... - 46 Optimizing... \ 47 Optimizing... - 48 Optimizing... / 49 Optimizing... - 50 Optimizing... \ 51 Optimizing... - 52 Optimizing... / 53 Optimizing... - 54 Optimizing... \ 55 Optimizing... - 56 Optimizing... / 57 Optimizing... - 58 Optimizing... \ 59 Optimizing... - 60 Optimizing... / 61 Optimizing... - 62 Optimizing... \ 63 Optimizing... - 64 Optimizing... / 65 Optimizing... - 66 Optimizing... \ 67 Optimizing... - 68 Optimizing... / 69 Optimizing... - 70 Optimizing... \ 71 Optimizing... - 72 Optimizing... / 73 Optimizing... - 74 Optimizing... \ 75 Optimizing... - 76 Optimizing... / 77 Optimizing... - 78 Optimizing... \ 79 Optimizing... - 80 Optimizing... / 81 Optimizing... - 82 Optimizing... \ 83 Optimizing... - 84 Optimizing... / 85 Optimizing... - 86 Optimizing... \ 87 Optimizing... - 88 Optimizing... / 89 Optimizing... - 90 Optimizing... \ 91 Optimizing... - 92 Optimizing... / 93 Optimizing... - 94 Optimizing... \ 95 Optimizing... - 96 Optimizing... / 97 Optimizing... - 98 Optimizing... \ 99 Optimizing... - 100 Optimizing... / 101 Optimizing... - 102 Optimizing... \ 103 Optimizing... - 104 Optimizing... / 105 Optimizing... - 106 Optimizing... \ 107 Optimizing... - 108 Optimizing... / 109 Optimizing... - 110 Optimizing... \ 111 Optimizing... - 112 +10: +10: 0.0942954 0.100879 +10: 0.498751 0.507798 +10: 0.318075 0.324244 +10: 0.675708 0.669691 +10: 0.0811184 0.0834898 +13/13 Test #10: test_simulations ................. Passed 344.96 sec 100% tests passed, 0 tests failed out of 13 -Total Test time (real) = 23.48 sec +Total Test time (real) = 345.13 sec make[1]: Leaving directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install - cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/libbpp-phyl-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/libbpp-phyl-2.4.1 -B/build/libbpp-phyl-2.4.1/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2572,9 +2615,9 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-8_amd64.deb'. dpkg-deb: building package 'libbpp-phyl12' in '../libbpp-phyl12_2.4.1-8_amd64.deb'. dpkg-deb: building package 'libbpp-phyl12-dbgsym' in '../libbpp-phyl12-dbgsym_2.4.1-8_amd64.deb'. +dpkg-deb: building package 'libbpp-phyl-dev' in '../libbpp-phyl-dev_2.4.1-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-phyl_2.4.1-8_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-phyl_2.4.1-8_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2582,12 +2625,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/4148063/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4148063/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/2862742 and its subdirectories -I: Current time: Fri May 19 07:48:45 -12 2023 -I: pbuilder-time-stamp: 1684525725 +I: removing directory /srv/workspace/pbuilder/4148063 and its subdirectories +I: Current time: Fri Jun 21 16:37:07 +14 2024 +I: pbuilder-time-stamp: 1718937427