Diff of the two buildlogs: -- --- b1/build.log 2025-08-28 18:23:26.883783923 +0000 +++ b2/build.log 2025-08-28 18:26:22.647978859 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Aug 28 06:20:43 -12 2025 -I: pbuilder-time-stamp: 1756405243 +I: Current time: Thu Oct 1 14:46:28 +14 2026 +I: pbuilder-time-stamp: 1790815588 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -35,53 +35,85 @@ 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/552255/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3580630/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +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 Oct 1 00:46 /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/3580630/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3580630/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='39728b03d94e4d228085c01f21706b6d' - 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='552255' - PS1='# ' - PS2='> ' + INVOCATION_ID=0a5781ccd9a74faf94c7a2c8f091762d + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=3580630 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.dYvMkbqy/pbuilderrc_oIKU --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dYvMkbqy/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + 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.dYvMkbqy/pbuilderrc_qJap --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.dYvMkbqy/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/552255/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3580630/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -451,7 +483,7 @@ Get: 304 http://deb.debian.org/debian forky/main arm64 libjam-java all 0.1.git20240425.aec45be+dfsg-1 [168 kB] Get: 305 http://deb.debian.org/debian forky/main arm64 libopenjfx-jni arm64 11.0.11+1-7 [19.7 MB] Get: 306 http://deb.debian.org/debian forky/main arm64 libopenjfx-java all 11.0.11+1-7 [8941 kB] -Fetched 345 MB in 3s (131 MB/s) +Fetched 345 MB in 1s (257 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (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 ... 19969 files and directories currently installed.) @@ -1471,8 +1503,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Aug 28 18:21:22 UTC 2025. -Universal Time is now: Thu Aug 28 18:21:22 UTC 2025. +Local time is now: Thu Oct 1 00:47:02 UTC 2026. +Universal Time is now: Thu Oct 1 00:47:02 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -1925,7 +1957,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+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_2.7.6+dfsg-1_source.changes +I: user script /srv/workspace/pbuilder/3580630/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/3580630/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/beast2-mcmc-2.7.6+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_2.7.6+dfsg-1_source.changes dpkg-buildpackage: info: source package beast2-mcmc dpkg-buildpackage: info: source version 2.7.6+dfsg-1 dpkg-buildpackage: info: source distribution unstable @@ -2058,7 +2094,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 15 seconds +Total time: 22 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' @@ -2137,7 +2173,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.981 seconds + [java] Total calculation time: 0.942 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 @@ -2169,7 +2205,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.036 seconds + [java] Total calculation time: 1.079 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 @@ -2201,14 +2237,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.927 seconds + [java] Total calculation time: 1.19 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712793 variance: 0.33333524355317856 ESS: 198672.26933150293 [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] @@ -2233,7 +2269,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.889 seconds + [java] Total calculation time: 1.007 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 @@ -2265,7 +2301,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.894 seconds + [java] Total calculation time: 0.918 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834576856 variance: 0.3333352435537048 ESS: 198672.26933242727 @@ -2382,50 +2418,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [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] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] trace log written to /tmp/bactrian.log [java] seq1: 3 4 [java] seq2: 3 4 @@ -2536,22 +2528,50 @@ [java] [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [java] 69 patterns - [java] - [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2715,28 +2735,22 @@ [java] Using character uncertainty in tree likelihood. [java] With 6 unique site patterns. [java] Using rescaling scheme : none - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] German_ST: 5051 2 [java] Dutch_List: 5051 2 [java] English_ST: 5051 2 @@ -2985,10 +2999,28 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 64 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 64 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3161,19 +3193,10 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 4.0.1 (PRE-RELEASE) resource 0: CPU (arm64) + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -3364,7 +3387,19 @@ [java] [java] =============================================================================== [java] Start likelihood: -14.297530455869882 - [java] End likelihood: -2.101581781210349 + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 @@ -3376,7 +3411,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.599 seconds + [java] Total calculation time: 0.618 seconds + [java] End likelihood: -2.101581781210349 [java] =============================================================================== [java] Citations for this model: [java] @@ -3402,7 +3438,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.469 seconds + [java] Total calculation time: 0.484 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3429,7 +3465,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.641 seconds + [java] Total calculation time: 0.635 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3455,7 +3491,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.959 seconds + [java] Total calculation time: 0.968 seconds [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3503,12 +3539,6 @@ [java] =============================================================================== [java] Start likelihood: 0.6286086594223761 [java] End likelihood: 3.119201359019653 - [java] Testing mirror distribution - [java] Testing mirror distribution for scaling - [java] kick in - [java] kick in - [java] kick in - [java] Testing mirror distribution [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(unknown) 0.46265 69697 930304 1.00000 0.06970 Try setting delta to about 0.231 @@ -3520,7 +3550,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.481 seconds + [java] Total calculation time: 0.462 seconds + [java] Testing mirror distribution + [java] Testing mirror distribution for scaling + [java] kick in + [java] kick in + [java] kick in + [java] Testing mirror distribution [java] Testing t4 s= 1.0013578565664571 [java] Testing bactrian_t4 s= 1.0001051250800803 [java] Testing bactrian_strawhat s= 0.25462688741501555 @@ -3544,227 +3580,6 @@ [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] 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.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [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$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [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.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [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$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [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 - [java] t1=10 [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -4018,6 +3833,227 @@ [java] [java] t0 = 0 (0.0) [java] t1 = 10 (10.0) + [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.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [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$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [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.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [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$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [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 + [java] t1=10 [java] Distribution lower = 0, upper = 6 windowSize = 1 Average deviation: 2957 [java] Distribution lower = 0, upper = 6 windowSize = 2 Average deviation: 2179 [java] Distribution lower = 0, upper = 6 windowSize = 3 Average deviation: 3318 @@ -4056,7 +4092,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.817 seconds + [java] Total calculation time: 0.868 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873523 variance: 0.9962228119352534 ESS: 194315.96975231904 @@ -4088,30 +4124,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.79 seconds + [java] Total calculation time: 0.806 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 [java] ------------------------------------------------- [java] [java] trace log written to /tmp/bactrian.log - [java] End likelihood: -0.8084620917497215 - [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. - [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] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] - [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [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] @@ -4134,6 +4153,23 @@ [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] + [java] End likelihood: -0.8084620917497215 + [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. + [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] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] + [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] =============================================================================== [java] Citations for this model: [java] @@ -4160,14 +4196,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.561 seconds + [java] Total calculation time: 3.669 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438963848 variance: 1.6815511765072393 ESS: 106131.3927120149 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.20113760213898557 + [java] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4263,11 +4299,6 @@ [java] Alignment(null): [taxa, patterns, sites] = [6, 50, 5051] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [6, 50, 5051] - [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] 9.094947017729282E-13 [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4310,6 +4341,11 @@ [java] 85 sites [java] 32 patterns [java] + [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] 9.094947017729282E-13 [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] [java] human: 768 4 @@ -4681,6 +4717,16 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] + [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] Dim = 5 [java] value[0] = 1.0 [java] value[1] = 2.0 @@ -4711,16 +4757,6 @@ [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 @@ -14492,242 +14528,6 @@ [java] Testing logNormal[M=3.7345735018263806 S=0.33097172629081073].pdf(0.5381197827356734) [java] Testing logNormal[M=2.7300763125005805 S=1.1398342630952363].pdf(2.1530245389086) [java] Testing logNormal[M=-4.004138588390202 S=7.156342751460897].pdf(0.8625064256425905) - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.base v2.7.6 - [java] java.lang.reflect.InvocationTargetException - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) - [java] at beast.base.core.Input.fromString(Unknown Source) - [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) - [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) - [java] at beast.base.core.BEASTObject.getInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listActiveBEASTObjects(Unknown Source) - [java] at beast.base.core.BEASTObjectStore.listActiveBEASTObjects(Unknown Source) - [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) - [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(Unknown Source) - [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [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$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] Caused by: java.lang.NumberFormatException: empty String - [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) - [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) - [java] at java.base/java.lang.Double.parseDouble(Double.java:792) - [java] at java.base/java.lang.Double.(Double.java:888) - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) - [java] ... 109 more - [java] java.lang.reflect.InvocationTargetException - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) - [java] at beast.base.core.Input.fromString(Unknown Source) - [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) - [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) - [java] at beast.base.core.BEASTObjectStore.listInputs(Unknown Source) - [java] at beast.base.parser.XMLProducer.beastObjectToXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) - [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(Unknown Source) - [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [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$7(TestMethodTestDescriptor.java:218) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) - [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) - [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) - [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) - [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) - [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) - [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) - [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) - [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) - [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) - [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) - [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) - [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) - [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) - [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] Caused by: java.lang.NumberFormatException: empty String - [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) - [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) - [java] at java.base/java.lang.Double.parseDouble(Double.java:792) - [java] at java.base/java.lang.Double.(Double.java:888) - [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) - [java] ... 106 more [java] Testing logNormal[M=-0.6327958730249152 S=5.9225222332215].pdf(1.1999226170794564) [java] Testing logNormal[M=-4.131441279512335 S=2.406772442072734].pdf(2.2299551419929737) [java] Testing logNormal[M=2.7294323947275148 S=2.2637022277391408].pdf(1.6029551111234437) @@ -14995,6 +14795,249 @@ [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 v2.7.6 + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.base v2.7.6 + [java] java.lang.reflect.InvocationTargetException + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) + [java] at beast.base.core.Input.fromString(Unknown Source) + [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) + [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) + [java] at beast.base.core.BEASTObject.getInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listActiveBEASTObjects(Unknown Source) + [java] at beast.base.core.BEASTObjectStore.listActiveBEASTObjects(Unknown Source) + [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) + [java] at beast.base.parser.ClassToPackageMap.getPackagesAndVersions(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(Unknown Source) + [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [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$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] Caused by: java.lang.NumberFormatException: empty String + [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) + [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) + [java] at java.base/java.lang.Double.parseDouble(Double.java:792) + [java] at java.base/java.lang.Double.(Double.java:888) + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) + [java] ... 109 more + [java] java.lang.reflect.InvocationTargetException + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:486) + [java] at beast.base.core.Input.fromString(Unknown Source) + [java] at beast.base.core.InputForAnnotatedConstructor.(Unknown Source) + [java] at beast.base.core.BEASTInterface.listAnnotatedInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.listInputs(Unknown Source) + [java] at beast.base.core.BEASTObjectStore.listInputs(Unknown Source) + [java] at beast.base.parser.XMLProducer.beastObjectToXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at beast.base.parser.XMLProducer.toXML(Unknown Source) + [java] at test.beast.util.XMLTest.testAnnotatedConstructor2(Unknown Source) + [java] at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:580) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) + [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$7(TestMethodTestDescriptor.java:218) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) + [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1596) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$execute$0(EngineExecutionOrchestrator.java:58) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.withInterceptedStreams(EngineExecutionOrchestrator.java:141) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:57) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:103) + [java] at org.junit.platform.launcher.core.DefaultLauncher.execute(DefaultLauncher.java:85) + [java] at org.junit.platform.launcher.core.DelegatingLauncher.execute(DelegatingLauncher.java:47) + [java] at org.junit.platform.launcher.core.SessionPerRequestLauncher.execute(SessionPerRequestLauncher.java:63) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.executeTests(ConsoleTestExecutor.java:102) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.lambda$execute$1(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.tasks.CustomContextClassLoaderExecutor.invoke(CustomContextClassLoaderExecutor.java:35) + [java] at org.junit.platform.console.tasks.ConsoleTestExecutor.execute(ConsoleTestExecutor.java:71) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:61) + [java] at org.junit.platform.console.options.ExecuteTestsCommand.execute(ExecuteTestsCommand.java:27) + [java] at org.junit.platform.console.options.BaseCommand.call(BaseCommand.java:74) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:129) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:93) + [java] at org.junit.platform.console.options.MainCommand.call(MainCommand.java:77) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.executeUserObject(CommandLine.java:1953) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.access$1300(CommandLine.java:145) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2352) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.handle(CommandLine.java:2314) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) + [java] at org.junit.platform.console.shadow.picocli.CommandLine$RunLast.execute(CommandLine.java:2316) + [java] at org.junit.platform.console.shadow.picocli.CommandLine.execute(CommandLine.java:2078) + [java] at org.junit.platform.console.options.MainCommand.runCommand(MainCommand.java:137) + [java] at org.junit.platform.console.options.MainCommand.run(MainCommand.java:125) + [java] at org.junit.platform.console.options.CommandFacade.run(CommandFacade.java:36) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) + [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) + [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) + [java] Caused by: java.lang.NumberFormatException: empty String + [java] at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:1842) + [java] at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110) + [java] at java.base/java.lang.Double.parseDouble(Double.java:792) + [java] at java.base/java.lang.Double.(Double.java:888) + [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:62) + [java] ... 106 more + [java] adfgad + [java] exception thrown + [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) + [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null + [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.DirectConstructorHandleAccessor.newInstance(DirectConstructorHandleAccessor.java:74) [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:502) @@ -15334,13 +15377,10 @@ [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] adfgad - [java] exception thrown - [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) - [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null - [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ @@ -15403,8 +15443,6 @@ [java] │ ├─ UncertainAlignmentTest ✔ [java] │ │ └─ testUncertainAlignment() ✔ [java] │ ├─ GeneralSubstitutionModelTest ✔ - [java] - [java] WARNING: Delegated to the 'execute' command. [java] │ │ └─ getTransitionProbabilities() ✔ [java] │ ├─ DeltaExchangeOperatorTest ✔ [java] │ │ ├─ testKeepsSum() ✔ @@ -15419,8 +15457,6 @@ [java] │ │ ├─ testHKY85GLikelihood() ✔ [java] │ │ ├─ testSDolloLikelihood() ✔ [java] │ │ ├─ testAminoAcidLikelihoodJTT() ✔ - [java] This behaviour has been deprecated and will be removed in a future release. - [java] Please use the 'execute' command directly. [java] │ │ ├─ testAminoAcidLikelihoodWAG() ✔ [java] │ │ ├─ testAminoAcidLikelihoodIMTRev() ✔ [java] │ │ ├─ testAminoAcidLikelihoodIcpRev() ✔ @@ -15550,7 +15586,7 @@ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 13045 ms ✔ + [java] │ │ └─ testCoalescentTimes() 12987 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ @@ -15607,7 +15643,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 77708 ms + [java] Test run finished after 79484 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15621,10 +15657,10 @@ [java] [ 207 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1118661053 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null629628372 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl [junitreport] Transform time: 407ms -[junitreport] Deleting: /tmp/null1118661053 +[junitreport] Deleting: /tmp/null629628372 junit-integration: [java] @@ -15633,16 +15669,12 @@ [java] Loading package BEAST.app v2.7.6 BEAST.app v2.7.6 BEAST.base v2.7.6 [java] Testing 160 classes [java] Done! - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.app v2.7.6 - [java] Loading package BEAST.base v2.7.6 [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus [java] exception thrown [java] Cannot read the array length because "" is null - [java] - [java] WARNING: Delegated to the 'execute' command. - [java] This behaviour has been deprecated and will be removed in a future release. - [java] Please use the 'execute' command directly. + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.app v2.7.6 + [java] Loading package BEAST.base v2.7.6 [java] [java] [java] @@ -15668,7 +15700,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 661 ms + [java] Test run finished after 650 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15682,10 +15714,14 @@ [java] [ 9 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1169341336 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1566521784 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl -[junitreport] Transform time: 115ms -[junitreport] Deleting: /tmp/null1169341336 +[junitreport] Transform time: 125ms +[junitreport] Deleting: /tmp/null1566521784 junit-xmlparsertest: [java] @@ -15698,7 +15734,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 295 ms + [java] Test run finished after 269 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15716,15 +15752,15 @@ [java] WARNING: Delegated to the 'execute' command. [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null942829400 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null496084255 [junitreport] Loading stylesheet ile:/usr/share/ant/lib/ant-junit.jar!/org/apache/tools/ant/taskdefs/optional/junit/xsl/junit-frames.xsl [junitreport] Transform time: 77ms -[junitreport] Deleting: /tmp/null942829400 +[junitreport] Deleting: /tmp/null496084255 junit: BUILD SUCCESSFUL -Total time: 1 minute 22 seconds +Total time: 1 minute 24 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15762,12 +15798,14 @@ 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/3580630/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3580630/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/552255 and its subdirectories -I: Current time: Thu Aug 28 06:23:25 -12 2025 -I: pbuilder-time-stamp: 1756405405 +I: removing directory /srv/workspace/pbuilder/3580630 and its subdirectories +I: Current time: Thu Oct 1 14:49:21 +14 2026 +I: pbuilder-time-stamp: 1790815761