Diff of the two buildlogs: -- --- b1/build.log 2024-04-23 08:02:50.059804486 +0000 +++ b2/build.log 2024-04-23 08:10:11.796946872 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Apr 22 19:59:25 -12 2024 -I: pbuilder-time-stamp: 1713859165 +I: Current time: Tue Apr 23 22:02:54 +14 2024 +I: pbuilder-time-stamp: 1713859374 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -38,52 +38,84 @@ 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/1034983/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2073426/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-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 Apr 23 08:03 /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/2073426/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2073426/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.21(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='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='12970a17b2034124b9cbf7f3d60c21c3' - 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='1034983' - PS1='# ' - PS2='> ' + INVOCATION_ID=b4377ecad23b4c66b3ac239b0d65d49b + 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=2073426 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.ecLpEbKo/pbuilderrc_Oj9e --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ecLpEbKo/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='109' - 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.ecLpEbKo/pbuilderrc_9pdF --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ecLpEbKo/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=109 + 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 codethink02-arm64 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-cloud-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:15 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1034983/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:16 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2073426/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -461,7 +493,7 @@ Get: 312 http://deb.debian.org/debian trixie/main arm64 libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 313 http://deb.debian.org/debian trixie/main arm64 libopenjfx-jni arm64 11.0.11+1-3.1 [19.0 MB] Get: 314 http://deb.debian.org/debian trixie/main arm64 libopenjfx-java all 11.0.11+1-3.1 [8903 kB] -Fetched 338 MB in 6s (52.5 MB/s) +Fetched 338 MB in 3s (99.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1: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 ... 19930 files and directories currently installed.) @@ -1498,8 +1530,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 23 08:00:15 UTC 2024. -Universal Time is now: Tue Apr 23 08:00:15 UTC 2024. +Local time is now: Tue Apr 23 08:05:11 UTC 2024. +Universal Time is now: Tue Apr 23 08:05:11 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:arm64 (0.40.0-4+b1) ... @@ -1951,7 +1983,11 @@ 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/2073426/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2073426/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 @@ -2070,7 +2106,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 22 seconds +Total time: 45 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' @@ -2149,14 +2185,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.084 seconds + [java] Total calculation time: 2.102 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] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -2181,7 +2217,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.106 seconds + [java] Total calculation time: 1.158 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 @@ -2213,13 +2249,12 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.984 seconds + [java] Total calculation time: 1.105 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] =============================================================================== [java] Citations for this model: @@ -2234,6 +2269,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -0.6931471805599453 + [java] End likelihood: -0.6931471805599453 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianIntervalOperator(unknown) 3.89367 611282 1388719 1.00000 0.30564 @@ -2245,7 +2281,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.953 seconds + [java] Total calculation time: 1.523 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 @@ -2277,12 +2313,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.927 seconds + [java] Total calculation time: 1.721 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834576856 variance: 0.3333352435537048 ESS: 198672.26933242727 [java] ------------------------------------------------- [java] + [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log [java] seq1: 3 4 [java] seq2: 3 4 @@ -2327,10 +2364,6 @@ [java] [java] transition prob : [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] - [java] row 0 prob sum = 0.9999999999999996 - [java] row 1 prob sum = 0.9999999999999998 - [java] row 2 prob sum = 0.9999999999999999 - [java] End likelihood: -0.6931471805599453 [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): [java] java.lang.IllegalArgumentException: Input 'weight' must be specified. [java] at beast.base.core.Input.validate(Unknown Source) @@ -2439,6 +2472,20 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== + [java] row 0 prob sum = 0.9999999999999996 + [java] row 1 prob sum = 0.9999999999999998 + [java] row 2 prob sum = 0.9999999999999999 + [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 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. @@ -2478,17 +2525,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [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 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -2541,6 +2577,29 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [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 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 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] 1.1368683772161603E-12 + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2571,29 +2630,19 @@ [java] Starting frequencies: [1.0, 0.0] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX 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 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 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] 1.1368683772161603E-12 - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [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. == @@ -2643,141 +2692,6 @@ [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 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using 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] Using 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 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 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 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 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 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 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 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 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 6 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [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] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2983,6 +2897,42 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [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: 3.1.2 resource 0: CPU + [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: [0.25, 0.25, 0.25, 0.25] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [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: 3.1.2 resource 0: CPU + [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: 3.1.2 resource 0: CPU + [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: 3.1.2 resource 0: CPU + [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. == @@ -2992,7 +2942,7 @@ [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] Using ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic @@ -3005,7 +2955,7 @@ [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] Using ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic @@ -3016,11 +2966,7 @@ [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] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -3029,12 +2975,25 @@ [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] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 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 69 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 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. == @@ -3042,8 +3001,12 @@ [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] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 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. == @@ -3051,12 +3014,25 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 8 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 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 8 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [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. == @@ -3064,11 +3040,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 64 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. + [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 64 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -3077,11 +3053,7 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. + [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -3090,7 +3062,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [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] ============================================================================================================== @@ -3099,7 +3075,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [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] ============================================================================================================== @@ -3121,7 +3101,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [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] ============================================================================================================== @@ -3132,42 +3116,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [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: 3.1.2 resource 0: CPU - [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: [0.25, 0.25, 0.25, 0.25] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [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: 3.1.2 resource 0: CPU - [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: 3.1.2 resource 0: CPU - [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: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [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 @@ -3245,6 +3193,59 @@ [java] 85 sites [java] 32 patterns [java] + [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 8 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 8 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] Using 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 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 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] Using BEAGLE version: 3.1.2 resource 0: CPU [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 @@ -3318,30 +3319,41 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] =============================================================================== - [java] Citations for this model: - [java] - [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, - [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, - [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, - [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, - [java] Alexei J. Drummond - [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. - [java] PLoS computational biology 15, no. 4 (2019): e1006650. - [java] - [java] =============================================================================== - [java] Start likelihood: -14.297530455869882 + [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 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using 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. == @@ -3378,9 +3390,32 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_NONE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] =============================================================================== + [java] Citations for this model: + [java] + [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, + [java] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, + [java] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, + [java] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, + [java] Alexei J. Drummond + [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. + [java] PLoS computational biology 15, no. 4 (2019): e1006650. + [java] + [java] =============================================================================== + [java] Start likelihood: -14.297530455869882 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) - [java] End likelihood: -2.101581781210349 [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 [java] [java] Tuning: The value of the operator's tuning parameter, or '-' if the operator can't be optimized. @@ -3390,7 +3425,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.607 seconds + [java] Total calculation time: 1.391 seconds + [java] End likelihood: -2.101581781210349 [java] =============================================================================== [java] Citations for this model: [java] @@ -3415,7 +3451,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.53 seconds + [java] Total calculation time: 0.643 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3430,7 +3466,6 @@ [java] =============================================================================== [java] Start likelihood: -21.446295683804824 [java] End likelihood: 0.008929267909451477 - [java] End likelihood: -0.5552616722623194 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.33125 153295 347047 0.50000 0.30638 @@ -3443,7 +3478,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.663 seconds + [java] Total calculation time: 0.805 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3457,7 +3492,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: -2.422052674651341 + [java] End likelihood: -0.5552616722623194 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -3469,7 +3504,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.982 seconds + [java] Total calculation time: 2.032 seconds + [java] End likelihood: -2.422052674651341 [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3527,7 +3563,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.466 seconds + [java] Total calculation time: 0.719 seconds [java] End likelihood: 3.119201359019653 [java] Testing mirror distribution [java] Testing mirror distribution for scaling @@ -3658,158 +3694,6 @@ [java] 2 taxa [java] 8 sites + 11241 constant sites [java] 10 patterns - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 12 patterns - [java] - [java] Filter 3:6:1 - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] human AACC - [java] 1chimp GTAC - [java] Filter 11:14:1 - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] human GGAA - [java] 1chimp GTAC - [java] Filter 3:16:4 - [java] 2 taxa - [java] 4 sites - [java] 3 patterns - [java] human ACGA - [java] 1chimp GGGG - [java] Filter 4:14:3 - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] human ACGA - [java] 1chimp TGCA - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] Filter 1 - [java] 2 taxa - [java] 1 sites - [java] 1 patterns - [java] Filter 2,5 - [java] 2 taxa - [java] 2 sites - [java] 2 patterns - [java] Filter 2,5,3,4 - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] Filter 1-9 - [java] 2 taxa - [java] 9 sites - [java] 9 patterns - [java] Filter 2-9 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 10- - [java] 2 taxa - [java] 7 sites - [java] 7 patterns - [java] Filter -10 - [java] 2 taxa - [java] 10 sites - [java] 10 patterns - [java] Filter - - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] Filter 2-5,7-10 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] Filter 1:16:2 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 2:16:2 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 1:10:2 - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] Filter 1::3 - [java] 2 taxa - [java] 6 sites - [java] 6 patterns - [java] Filter 2::3 - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] Filter :: - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] Filter 2:5: - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] Filter :5: - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] Filter 1::3,2::3 - [java] 2 taxa - [java] 11 sites - [java] 11 patterns - [java] Filter 3::3 - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] t0: 1 4 - [java] t1: 1 4 - [java] Alignment(null) - [java] 2 taxa - [java] 1 site - [java] - [java] t0 = 0 (10.0) - [java] t1 = 10 (0.0) - [java] t0: 1 4 - [java] t1: 1 4 - [java] Alignment(null) - [java] 2 taxa - [java] 1 site - [java] - [java] t0 = null (0.0) - [java] t1 = 10 (0.0) - [java] t0: 1 4 - [java] t1: 1 4 - [java] Alignment(null) - [java] 2 taxa - [java] 1 site - [java] - [java] t0 = 0 (0.0) - [java] t1 = 10 (10.0) [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] @@ -4032,6 +3916,158 @@ [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] [java] t0=0 [java] t1=10 + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 12 patterns + [java] + [java] Filter 3:6:1 + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] human AACC + [java] 1chimp GTAC + [java] Filter 11:14:1 + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] human GGAA + [java] 1chimp GTAC + [java] Filter 3:16:4 + [java] 2 taxa + [java] 4 sites + [java] 3 patterns + [java] human ACGA + [java] 1chimp GGGG + [java] Filter 4:14:3 + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] human ACGA + [java] 1chimp TGCA + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] Filter 1 + [java] 2 taxa + [java] 1 sites + [java] 1 patterns + [java] Filter 2,5 + [java] 2 taxa + [java] 2 sites + [java] 2 patterns + [java] Filter 2,5,3,4 + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] Filter 1-9 + [java] 2 taxa + [java] 9 sites + [java] 9 patterns + [java] Filter 2-9 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 10- + [java] 2 taxa + [java] 7 sites + [java] 7 patterns + [java] Filter -10 + [java] 2 taxa + [java] 10 sites + [java] 10 patterns + [java] Filter - + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] Filter 2-5,7-10 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] Filter 1:16:2 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 2:16:2 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 1:10:2 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter 1::3 + [java] 2 taxa + [java] 6 sites + [java] 6 patterns + [java] Filter 2::3 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter :: + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] Filter 2:5: + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] Filter :5: + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter 1::3,2::3 + [java] 2 taxa + [java] 11 sites + [java] 11 patterns + [java] Filter 3::3 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = 0 (10.0) + [java] t1 = 10 (0.0) + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = null (0.0) + [java] t1 = 10 (0.0) + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = 0 (0.0) + [java] t1 = 10 (10.0) [java] t1=10 [java] WARNING: no trait specified for t0: Assumed to be 10.0 [java] t0=0 @@ -4074,7 +4110,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 0.914 seconds + [java] Total calculation time: 2.135 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873523 variance: 0.9962228119352534 ESS: 194315.96975231904 @@ -4106,7 +4142,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.242 seconds + [java] Total calculation time: 0.895 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 @@ -4119,6 +4155,22 @@ [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] 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] @@ -4136,22 +4188,6 @@ [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] 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] @@ -4178,7 +4214,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.838 seconds + [java] Total calculation time: 4.822 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438963848 variance: 1.6815511765072393 ESS: 106131.3927120149 @@ -4186,6 +4222,10 @@ [java] [java] End likelihood: -0.20113760213898557 [java] trace log written to /tmp/bactrian.log + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] Starting frequencies: [0.074, 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 @@ -4197,11 +4237,6 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] 9.094947017729282E-13 [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -4270,6 +4305,7 @@ [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] + [java] 9.094947017729282E-13 [java] German_ST: 5051 2 [java] Dutch_List: 5051 2 [java] English_ST: 5051 2 @@ -4678,16 +4714,6 @@ [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] [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] t 0=0 - [java] t 1=1 - [java] t 2=2 - [java] t 3=3 - [java] t 4=4 - [java] t 5=5 - [java] t 6=6 - [java] t 7=7 - [java] t 8=8 - [java] t 9=9 [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -4739,6 +4765,16 @@ [java] t 7 = 7 (7.0) [java] t 8 = 8 (8.0) [java] t 9 = 9 (9.0) + [java] t 0=0 + [java] t 1=1 + [java] t 2=2 + [java] t 3=3 + [java] t 4=4 + [java] t 5=5 + [java] t 6=6 + [java] t 7=7 + [java] t 8=8 + [java] t 9=9 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -14202,249 +14238,7 @@ [java] Testing logNormal[M=-3.8592406916852773 S=4.675654282248901].pdf(1.327026117841463) [java] Testing logNormal[M=0.9734890545081489 S=4.191218043531812].pdf(2.2421231243611857) [java] Testing logNormal[M=-1.6790946511169147 S=9.51512169711551].pdf(1.4347169245582674) - [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.NativeConstructorAccessorImpl.newInstance0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) - [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.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$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:651) - [java] at java.base/java.lang.Double.(Double.java:733) - [java] ... 114 more - [java] java.lang.reflect.InvocationTargetException - [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) - [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) - [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) - [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.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] Testing logNormal[M=-1.811010817208989 S=2.1487360251489918].pdf(1.6871128737277807) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$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:651) - [java] at java.base/java.lang.Double.(Double.java:733) - [java] ... 111 more - [java] + [java] Testing logNormal[M=-1.811010817208989 S=2.1487360251489918].pdf(1.6871128737277807) [java] Testing logNormal[M=-0.40462451838701163 S=5.421521361968216].pdf(2.033745931958869) [java] Testing logNormal[M=4.229626403465932 S=0.04843810643724189].pdf(1.0131268983623594) [java] Testing logNormal[M=-0.03759524693876415 S=3.4027106758882573].pdf(1.1331409497140275) @@ -15019,6 +14813,248 @@ [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.NativeConstructorAccessorImpl.newInstance0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) + [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.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$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:651) + [java] at java.base/java.lang.Double.(Double.java:733) + [java] ... 114 more + [java] java.lang.reflect.InvocationTargetException + [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) + [java] at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499) + [java] at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:480) + [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.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at java.base/java.util.ArrayList.forEach(ArrayList.java:1511) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:155) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) + [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) + [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) + [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) + [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) + [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$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:651) + [java] at java.base/java.lang.Double.(Double.java:733) + [java] ... 111 more [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) @@ -15259,6 +15295,13 @@ [java] at java.base/java.lang.Double.parseDouble(Double.java:651) [java] at java.base/java.lang.Double.(Double.java:733) [java] ... 113 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] beast.base.evolution.tree.TreeParser$TreeParsingException: Duplicate taxon found: A [java] at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitTree(Unknown Source) [java] at beast.base.evolution.tree.TreeParser$NewickASTVisitor.visitTree(Unknown Source) @@ -15366,13 +15409,10 @@ [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 ✔ @@ -15413,10 +15453,6 @@ [java] │ │ └─ testScientificNotationIntTooLarge() ✔ [java] │ ├─ IntegerParameterListTest ✔ [java] │ │ └─ test1() ✔ - [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] │ ├─ SumTest ✔ [java] │ │ └─ testSum() ✔ [java] │ ├─ OperatorScheduleTest ✔ @@ -15536,7 +15572,7 @@ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 10498 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 16192 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15582,7 +15618,7 @@ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 13563 ms ✔ + [java] │ │ └─ testCoalescentTimes() 19243 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ @@ -15639,7 +15675,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 83533 ms + [java] Test run finished after 138596 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15653,10 +15689,10 @@ [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/null1328365617 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null832756483 [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: 1019ms -[junitreport] Deleting: /tmp/null1328365617 +[junitreport] Transform time: 1231ms +[junitreport] Deleting: /tmp/null832756483 junit-integration: [java] @@ -15665,12 +15701,12 @@ [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] 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] @@ -15696,7 +15732,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1443 ms + [java] Test run finished after 2105 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15714,10 +15750,10 @@ [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/null481359814 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1057510642 [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: 340ms -[junitreport] Deleting: /tmp/null481359814 +[junitreport] Transform time: 388ms +[junitreport] Deleting: /tmp/null1057510642 junit-xmlparsertest: [java] @@ -15730,7 +15766,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 698 ms + [java] Test run finished after 671 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15748,15 +15784,15 @@ [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/null362630173 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null743325540 [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: 252ms -[junitreport] Deleting: /tmp/null362630173 +[junitreport] Transform time: 268ms +[junitreport] Deleting: /tmp/null743325540 junit: BUILD SUCCESSFUL -Total time: 1 minute 32 seconds +Total time: 2 minutes 32 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15794,12 +15830,14 @@ 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/2073426/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2073426/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/1034983 and its subdirectories -I: Current time: Mon Apr 22 20:02:47 -12 2024 -I: pbuilder-time-stamp: 1713859367 +I: removing directory /srv/workspace/pbuilder/2073426 and its subdirectories +I: Current time: Tue Apr 23 22:10:08 +14 2024 +I: pbuilder-time-stamp: 1713859808