Diff of the two buildlogs: -- --- b1/build.log 2023-04-16 14:15:23.218793303 +0000 +++ b2/build.log 2023-04-16 14:30:48.789741232 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 16 02:11:04 -12 2023 -I: pbuilder-time-stamp: 1681654264 +I: Current time: Sun May 19 10:38:28 +14 2024 +I: pbuilder-time-stamp: 1716064708 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: copying [./beast2-mcmc_2.7.3+dfsg.orig.tar.xz] I: copying [./beast2-mcmc_2.7.3+dfsg-1.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Dec 20 08:11:42 2022 -12 +gpgv: Signature made Wed Dec 21 10:11:42 2022 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -39,135 +39,167 @@ dpkg-source: info: applying skip_install_BEAST_package.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3007034/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2592506/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 19 10:39 /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/2592506/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2592506/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='e4d6482a204c494d91af8211467e3fc5' - 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='3007034' - PS1='# ' - PS2='> ' + INVOCATION_ID=16c09006ef734aa7a2b29e92b2afd33b + 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=2592506 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.fYnnIEi1/pbuilderrc_n4A5 --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.fYnnIEi1/b1 --logfile b1/build.log beast2-mcmc_2.7.3+dfsg-1.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.fYnnIEi1/pbuilderrc_h7dQ --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.fYnnIEi1/b2 --logfile b2/build.log --extrapackages usrmerge beast2-mcmc_2.7.3+dfsg-1.dsc' + SUDO_GID=111 + SUDO_UID=106 + 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 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-0.deb11.5-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.12-1~bpo11+1 (2023-03-05) x86_64 GNU/Linux I: ls -l /bin total 5632 - -rwxr-xr-x 1 root root 1265648 Feb 12 08:05 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 Feb 12 08:05 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 04:31 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 04:31 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/3007034/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1265648 Feb 13 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 Feb 13 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 May 19 10:39 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/2592506/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -544,7 +576,7 @@ Get: 311 http://deb.debian.org/debian bookworm/main amd64 libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 312 http://deb.debian.org/debian bookworm/main amd64 libopenjfx-jni amd64 11.0.11+1-3 [22.1 MB] Get: 313 http://deb.debian.org/debian bookworm/main amd64 libopenjfx-java all 11.0.11+1-3 [8903 kB] -Fetched 519 MB in 15s (34.4 MB/s) +Fetched 519 MB in 25s (20.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libargon2-1: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.) @@ -2012,8 +2044,19 @@ 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/beast2-mcmc-2.7.3+dfsg/ && 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 > ../beast2-mcmc_2.7.3+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/2592506/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/2592506/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/beast2-mcmc-2.7.3+dfsg/ && 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 > ../beast2-mcmc_2.7.3+dfsg-1_source.changes dpkg-buildpackage: info: source package beast2-mcmc dpkg-buildpackage: info: source version 2.7.3+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2115,7 +2158,7 @@ [jar] Building jar: /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 25 seconds +Total time: 1 minute 33 seconds make[1]: Leaving directory '/build/beast2-mcmc-2.7.3+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/beast2-mcmc-2.7.3+dfsg' @@ -2191,7 +2234,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.647 seconds + [java] Total calculation time: 3.912 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.993665202588076 variance: 1.6192894315844928 ESS: 40484.42378045953 @@ -2223,14 +2266,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.63 seconds + [java] Total calculation time: 4.951 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326598056 variance: 0.00998468201961599 ESS: 199303.5697419037 [java] ------------------------------------------------- [java] - [java] End likelihood: 1.3580153849811107 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: 1.3580153849811107 [java] =============================================================================== [java] Citations for this model: [java] @@ -2255,7 +2298,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.452 seconds + [java] Total calculation time: 5.591 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712321 variance: 0.33333524355318095 ESS: 198672.26933150744 @@ -2287,14 +2330,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.441 seconds + [java] Total calculation time: 5.59 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.0000858829347083 variance: 0.3333352435532249 ESS: 198672.2693314681 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.6931471805599453 [java] =============================================================================== [java] Citations for this model: [java] @@ -2319,13 +2362,16 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.449 seconds + [java] Total calculation time: 6.828 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834570785 variance: 0.3333352435537157 ESS: 198672.26933227608 [java] ------------------------------------------------- [java] [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.6931471805599453 + [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): + [java] java.lang.IllegalArgumentException: Input 'weight' must be specified. [java] seq1: 3 4 [java] seq2: 3 4 [java] seq3: 3 4 @@ -2372,9 +2418,15 @@ [java] row 0 prob sum = 0.9999999999999996 [java] row 1 prob sum = 0.9999999999999998 [java] row 2 prob sum = 0.9999999999999999 - [java] End likelihood: -0.6931471805599453 - [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): - [java] java.lang.IllegalArgumentException: Input 'weight' must be specified. + [java] =============================================================================== + [java] Citations for this model: + [java] + [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, + [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, + [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, + [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, + [java] Alexei J. Drummond + [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. [java] at beast.base.core.Input.validate(Unknown Source) [java] at beast.base.core.BEASTInterface.validateInputs(Unknown Source) [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) @@ -2452,15 +2504,6 @@ [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) - [java] =============================================================================== - [java] Citations for this model: - [java] - [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, - [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, - [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, - [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, - [java] Alexei J. Drummond - [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. [java] PLoS computational biology 15, no. 4 (2019): e1006650. [java] [java] =============================================================================== @@ -2476,7 +2519,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.961 seconds + [java] Total calculation time: 4.464 seconds [java] End likelihood: -2.1015817812114337 [java] =============================================================================== [java] Citations for this model: @@ -2491,6 +2534,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -7.148765227934941 + [java] End likelihood: 0.008929267909651761 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.31053 307447 692554 1.00000 0.30745 @@ -2502,8 +2546,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.787 seconds - [java] End likelihood: 0.008929267909651761 + [java] Total calculation time: 2.167 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -2530,7 +2573,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.033 seconds + [java] Total calculation time: 2.852 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -2544,7 +2587,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: -2.422052674650429 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -2556,7 +2598,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.775 seconds + [java] Total calculation time: 4.342 seconds + [java] End likelihood: -2.422052674650429 [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -2614,7 +2657,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.41 seconds + [java] Total calculation time: 2.216 seconds [java] End likelihood: 3.1192013590196357 [java] Testing mirror distribution [java] Testing mirror distribution for scaling @@ -2644,17 +2687,6 @@ [java] Testing bactrian_triangle s= 0.999423750532334 [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 - [java] Testing bactrian_box s= 0.9993638943013682 - [java] Number of weights (4) does not match sequence length (16) - [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] - [java] 0human AAAACCCCGGGGTTTT - [java] 1chimp ACGTACGTACGTACGT - [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] - [java] AAAACCCCTTTTGGGG - [java] ACTGACGTACGTACGT - [java] [101000, 10000, 1, 110] - [java] GGGAAA - [java] AGGACA [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -2718,6 +2750,180 @@ [java] 16 sites with weight 12514 [java] 16 patterns [java] + [java] Testing bactrian_box s= 0.9993638943013682 + [java] Number of weights (4) does not match sequence length (16) + [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] + [java] 0human AAAACCCCGGGGTTTT + [java] 1chimp ACGTACGTACGTACGT + [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] AAAACCCCTTTTGGGG + [java] ACTGACGTACGTACGT + [java] [101000, 10000, 1, 110] + [java] GGGAAA + [java] AGGACA + [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727) + [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86) + [java] at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:66) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$0(ConsoleTestExecutor.java:58) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:33) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:58) + [java] at org.junit.platform.console.ConsoleLauncher.executeTests(ConsoleLauncher.java:120) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:82) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) + [java] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727) + [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) + [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) + [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) + [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86) + [java] at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:66) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$0(ConsoleTestExecutor.java:58) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:33) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:58) + [java] at org.junit.platform.console.ConsoleLauncher.executeTests(ConsoleLauncher.java:120) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:82) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) + [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) + [java] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] + [java] <0> <1> <2> <3> removed 6 sites + [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] + [java] t0=0 + [java] t1=10 [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -2908,169 +3114,6 @@ [java] [java] t0 = 0 (0.0) [java] t1 = 10 (10.0) - [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727) - [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86) - [java] at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:66) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$0(ConsoleTestExecutor.java:58) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:33) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:58) - [java] at org.junit.platform.console.ConsoleLauncher.executeTests(ConsoleLauncher.java:120) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:82) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) - [java] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:727) - [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestableMethod(TimeoutExtension.java:147) - [java] at org.junit.jupiter.engine.extension.TimeoutExtension.interceptTestMethod(TimeoutExtension.java:86) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker$ReflectiveInterceptorCall.lambda$ofVoidMethod$0(InterceptingExecutableInvoker.java:103) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.lambda$invoke$0(InterceptingExecutableInvoker.java:93) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:217) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:213) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:138) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:68) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:147) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:127) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:90) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:55) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:102) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:54) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:114) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:86) - [java] at org.junit.platform.launcher.core.DefaultLauncherSession$DelegatingLauncher.execute(DefaultLauncherSession.java:86) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:53) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:66) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$0(ConsoleTestExecutor.java:58) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:33) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:58) - [java] at org.junit.platform.console.ConsoleLauncher.executeTests(ConsoleLauncher.java:120) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:82) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) - [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) - [java] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] - [java] <0> <1> <2> <3> removed 6 sites - [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] - [java] t0=0 - [java] t1=10 [java] t1=10 [java] WARNING: no trait specified for t0: Assumed to be 10.0 [java] t0=0 @@ -3113,14 +3156,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.513 seconds + [java] Total calculation time: 4.739 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873339 variance: 0.9962228119352623 ESS: 194315.96975230493 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.9585015029579731 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.9585015029579731 [java] =============================================================================== [java] Citations for this model: [java] @@ -3145,15 +3188,22 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.459 seconds + [java] Total calculation time: 3.495 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.993665202588076 variance: 1.6192894315844928 ESS: 40484.42378045953 [java] ------------------------------------------------- [java] + [java] End likelihood: 0.043370341679253466 [java] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] + [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -3187,13 +3237,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -6.753673320834167 - [java] End likelihood: 0.043370341679253466 - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] - [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. @@ -3217,7 +3260,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 7.517 seconds + [java] Total calculation time: 23.789 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.001920911870047 variance: 1.6665559107038947 ESS: 24079.915120491776 @@ -3236,6 +3279,10 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -3277,10 +3324,6 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3292,6 +3335,7 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [java] 1.1368683772161603E-12 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -3433,7 +3477,6 @@ [java] [java] Tree A: [java] Without tip likelihoods: - [java] 1.1368683772161603E-12 [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [3, 3, 3] [java] -11.853202336328778 @@ -3695,16 +3738,6 @@ [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] - [java] t 0=0 - [java] t 1=1 - [java] t 2=2 - [java] t 3=3 - [java] t 4=4 - [java] t 5=5 - [java] t 6=6 - [java] t 7=7 - [java] t 8=8 - [java] t 9=9 [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -3778,6 +3811,16 @@ [java] t 7 = 7 (7.0) [java] t 8 = 8 (8.0) [java] t 9 = 9 (9.0) + [java] t 0=0 + [java] t 1=1 + [java] t 2=2 + [java] t 3=3 + [java] t 4=4 + [java] t 5=5 + [java] t 6=6 + [java] t 7=7 + [java] t 8=8 + [java] t 9=9 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -13589,8 +13632,6 @@ [java] Testing logNormal[M=-4.345440143381979 S=3.2615991283321675].pdf(1.3490390210390064) [java] Testing logNormal[M=-1.8195325460467937 S=3.7748939649434].pdf(1.8669817284936352) [java] Testing logNormal[M=2.085547860756294 S=5.924951447431691].pdf(2.19588868818812) - [java] Loading package BEAST.app v2.7.3 - [java] Loading package BEAST.app v2.7.3 [java] Testing logNormal[M=-3.059725410972325 S=2.386869513221023].pdf(1.904494983622476) [java] Testing logNormal[M=0.6806042597764801 S=2.2106986386588767].pdf(1.8973318071612364) [java] Testing logNormal[M=3.8232044516401515 S=4.788665410916259].pdf(1.882148438703016) @@ -13818,6 +13859,8 @@ [java] Testing logNormal[M=-2.023496228033016 S=3.9227618715869506].pdf(1.5882725769254962) [java] Testing logNormal[M=-3.577699957972137 S=9.345578106358118].pdf(2.165879097028796) [java] Testing logNormal[M=1.0516748055181635 S=5.484242020370206].pdf(1.6803895137128866) + [java] Loading package BEAST.app v2.7.3 + [java] Loading package BEAST.app v2.7.3 [java] Loading package BEAST.base v2.7.3 [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) @@ -14010,7 +14053,6 @@ [java] at java.base/java.lang.Double.parseDouble(Double.java:651) [java] at java.base/java.lang.Double.(Double.java:733) [java] ... 87 more - [java] adfgad [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) @@ -14286,6 +14328,7 @@ [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:55) [java] at org.junit.platform.console.ConsoleLauncher.execute(ConsoleLauncher.java:48) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:42) + [java] adfgad [java] exception thrown [java] /build/beast2-mcmc-2.7.3+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) [java] Test Nexus Examples in /build/beast2-mcmc-2.7.3+dfsg/beastfx/examples/nexus @@ -14347,11 +14390,11 @@ [java] │ │ ├─ testOperatorSchedulePlain() ✔ [java] │ │ └─ testOperatorScheduleNestedByRelativeWeight2() ✔ [java] │ ├─ BactrianIntervalOperatorTest ✔ - [java] │ │ ├─ testLogNormalDistribution() ✔ - [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ ├─ testUniformDistributionZeroUpperBound() ✔ - [java] │ │ ├─ testUniformDistribution() ✔ - [java] │ │ └─ testUniformDistributionZeroLowerBound() ✔ + [java] │ │ ├─ testLogNormalDistribution() 13120 ms ✔ + [java] │ │ ├─ testNormalDistribution() 14888 ms ✔ + [java] │ │ ├─ testUniformDistributionZeroUpperBound() 16456 ms ✔ + [java] │ │ ├─ testUniformDistribution() 19426 ms ✔ + [java] │ │ └─ testUniformDistributionZeroLowerBound() 18423 ms ✔ [java] │ ├─ DataTypeDeEncodeTest ✔ [java] │ │ └─ testDataTypeDeEncode() ✔ [java] │ ├─ UncertainAlignmentTest ✔ @@ -14370,9 +14413,9 @@ [java] │ │ ├─ testScaleAllIndependentlylDistribution() ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() ✔ - [java] │ │ └─ testNarrowExchange6Taxa() ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() 17669 ms ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() 16386 ms ✔ + [java] │ │ └─ testNarrowExchange6Taxa() 20147 ms ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ @@ -14409,16 +14452,16 @@ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ [java] │ │ ├─ testIntRandomWalkDistribution3x6() ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() 16690 ms ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() 17840 ms ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() ✔ + [java] │ │ ├─ testNormalDistribution() 12119 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 13296 ms ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 18522 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 63199 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -14464,7 +14507,7 @@ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 19465 ms ✔ + [java] │ │ └─ testCoalescentTimes() 70816 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ @@ -14521,7 +14564,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 135795 ms + [java] Test run finished after 381857 ms [java] [ 50 containers found ] [java] [ 0 containers skipped ] [java] [ 50 containers started ] @@ -14535,21 +14578,21 @@ [java] [ 173 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null775633389 +[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1277999610 [junitreport] Loading stylesheet jar:file:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 733ms -[junitreport] Deleting: /tmp/null775633389 +[junitreport] Transform time: 2048ms +[junitreport] Deleting: /tmp/null1277999610 junit-integration: [java] Loading package BEAST.app v2.7.3 BEAST.app v2.7.3 BEAST.base v2.7.3 [java] Testing 159 classes [java] Done! - [java] Test Nexus Examples in /build/beast2-mcmc-2.7.3+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null [java] Loading package BEAST.app v2.7.3 [java] Loading package BEAST.app v2.7.3 [java] Loading package BEAST.base v2.7.3 + [java] Test Nexus Examples in /build/beast2-mcmc-2.7.3+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null [java] [java] [java] @@ -14578,7 +14621,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 911 ms + [java] Test run finished after 2838 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -14592,10 +14635,10 @@ [java] [ 9 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null8187926 +[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1711891810 [junitreport] Loading stylesheet jar:file:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 196ms -[junitreport] Deleting: /tmp/null8187926 +[junitreport] Transform time: 629ms +[junitreport] Deleting: /tmp/null1711891810 junit-xmlparsertest: [java] @@ -14608,7 +14651,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 421 ms + [java] Test run finished after 1662 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -14622,15 +14665,15 @@ [java] [ 1 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null344326271 +[junitreport] Processing /build/beast2-mcmc-2.7.3+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null430415335 [junitreport] Loading stylesheet jar:file:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 120ms -[junitreport] Deleting: /tmp/null344326271 +[junitreport] Transform time: 530ms +[junitreport] Deleting: /tmp/null430415335 junit: BUILD SUCCESSFUL -Total time: 2 minutes 22 seconds +Total time: 6 minutes 41 seconds make[1]: Leaving directory '/build/beast2-mcmc-2.7.3+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -14659,8 +14702,8 @@ dpkg-gencontrol: warning: Depends field of package beast2-mcmc-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.3+dfsg-1_all.deb'. dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.7.3+dfsg-1_all.deb'. +dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.3+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../beast2-mcmc_2.7.3+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -O../beast2-mcmc_2.7.3+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -14668,12 +14711,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2592506/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2592506/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/3007034 and its subdirectories -I: Current time: Sun Apr 16 02:15:22 -12 2023 -I: pbuilder-time-stamp: 1681654522 +I: removing directory /srv/workspace/pbuilder/2592506 and its subdirectories +I: Current time: Sun May 19 10:53:50 +14 2024 +I: pbuilder-time-stamp: 1716065630