Diff of the two buildlogs: -- --- b1/build.log 2024-04-11 22:46:35.320516598 +0000 +++ b2/build.log 2024-04-11 22:58:18.698574736 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Apr 11 10:29:23 -12 2024 -I: pbuilder-time-stamp: 1712874563 +I: Current time: Fri Apr 12 12:46:46 +14 2024 +I: pbuilder-time-stamp: 1712875606 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/3576/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/498/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +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 11 22:47 /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/498/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/498/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='53f32c4ca17f4d18b504bca718b0eff7' - 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='3576' - PS1='# ' - PS2='> ' + INVOCATION_ID=1049ff75539d4e66a6203c03069eb448 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=498 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.f88IYEZV/pbuilderrc_FKz9 --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.f88IYEZV/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.f88IYEZV/pbuilderrc_YE53 --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.f88IYEZV/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux ff4a 6.1.0-18-armmp-lpae #1 SMP Debian 6.1.76-1 (2024-02-01) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-arm64 #1 SMP Debian 6.1.76-1 (2024-02-01) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 11 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/3576/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 11 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/498/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 armhf libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 313 http://deb.debian.org/debian trixie/main armhf libopenjfx-jni armhf 11.0.11+1-3.1 [18.0 MB] Get: 314 http://deb.debian.org/debian trixie/main armhf libopenjfx-java all 11.0.11+1-3.1 [8903 kB] -Fetched 324 MB in 21s (15.2 MB/s) +Fetched 324 MB in 7s (49.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19635 files and directories currently installed.) @@ -1498,8 +1530,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Apr 11 22:32:34 UTC 2024. -Universal Time is now: Thu Apr 11 22:32:34 UTC 2024. +Local time is now: Thu Apr 11 22:48:56 UTC 2024. +Universal Time is now: Thu Apr 11 22:48:56 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libdconf1:armhf (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/498/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/498/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: 2 minutes 16 seconds +Total time: 1 minute 3 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' @@ -2093,6 +2129,14 @@ [java] 768 sites [java] 69 patterns [java] + [java] OK + [java] test getCitation + [java] test initByName + [java] test listInputs + [java] test initByName + [java] test getInputValue + [java] test getOutputs + [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2104,23 +2148,15 @@ [java] 768 sites [java] 69 patterns [java] - [java] OK - [java] test getCitation - [java] test initByName - [java] test listInputs - [java] test initByName - [java] test getInputValue - [java] test getOutputs - [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): - [java] Writing file beast.log - [java] Sample null.1 null.2 - [java] 1 0.3 0.7 -- [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", [java] p: [ [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [1.0, 3.0] }, [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } [java] ] [java] } + [java] Writing file beast.log + [java] Sample null.1 null.2 + [java] 1 0.3 0.7 -- [java] Failed to set the string value to '1e-1' for beastobject id=null [java] Failed to set the string value to '21474836470' for beastobject id=null [java] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. @@ -2177,14 +2213,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.634 seconds + [java] Total calculation time: 3.059 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] @@ -2209,7 +2245,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.552 seconds + [java] Total calculation time: 3.073 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 @@ -2241,12 +2277,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.942 seconds + [java] Total calculation time: 2.955 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: @@ -2261,7 +2298,6 @@ [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 @@ -2273,12 +2309,13 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.741 seconds + [java] Total calculation time: 2.725 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 [java] ------------------------------------------------- [java] + [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: @@ -2293,7 +2330,6 @@ [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 @@ -2305,13 +2341,12 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.822 seconds + [java] Total calculation time: 2.761 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] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] [java] freqs = @@ -2331,6 +2366,115 @@ [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) + [java] at beast.base.core.BEASTInterface.validateInputs(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.operator.DeltaExchangeOperatorTest.testCanOperate(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] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [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 @@ -2340,31 +2484,12 @@ [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] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX [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: EIGEN_COMPLEX - [java] human: 772 4 - [java] chimp: 772 4 - [java] bonobo: 772 4 - [java] gorilla: 772 4 - [java] orangutan: 772 4 - [java] siamang: 772 4 - [java] Alignment(null) - [java] 6 taxa - [java] 772 sites with weight 145 - [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [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. @@ -2400,6 +2525,20 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] human: 772 4 + [java] chimp: 772 4 + [java] bonobo: 772 4 + [java] gorilla: 772 4 + [java] orangutan: 772 4 + [java] siamang: 772 4 + [java] Alignment(null) + [java] 6 taxa + [java] 772 sites with weight 145 + [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2535,6 +2674,37 @@ [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. == + [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] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic [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 @@ -2557,24 +2727,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [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] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2597,19 +2749,6 @@ [java] 768 sites [java] 69 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 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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -2639,8 +2778,6 @@ [java] 85 sites [java] 32 patterns [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2663,64 +2800,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] seq1: 3 4 - [java] seq2: 3 4 - [java] seq3: 3 4 - [java] Alignment(null) - [java] 3 taxa - [java] 3 sites - [java] 3 patterns - [java] - [java] seq1: 3 4 - [java] seq2: 3 4 - [java] seq3: 3 4 - [java] Alignment(null) - [java] 3 taxa - [java] 3 sites - [java] 3 patterns - [java] - [java] Most probable sequences: - [java] ATT - [java] ATC - [java] GCC - [java] - [java] Tree A: - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -11.85320233632878 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -11.85320233632878 - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -11.85320233632878 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.069603116476458 - [java] - [java] Tree B: - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -12.421114302827698 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE - [java] -11.621056623105131 - [java] - [java] Testing alignment doubling: [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2799,6 +2878,75 @@ [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: EIGEN_COMPLEX + [java] seq1: 3 4 + [java] seq2: 3 4 + [java] seq3: 3 4 + [java] Alignment(null) + [java] 3 taxa + [java] 3 sites + [java] 3 patterns + [java] + [java] seq1: 3 4 + [java] seq2: 3 4 + [java] seq3: 3 4 + [java] Alignment(null) + [java] 3 taxa + [java] 3 sites + [java] 3 patterns + [java] + [java] Most probable sequences: + [java] ATT + [java] ATC + [java] GCC + [java] + [java] Tree A: + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -11.85320233632878 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -11.85320233632878 + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -11.85320233632878 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.069603116476458 + [java] + [java] Tree B: + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -12.421114302827698 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE + [java] -11.621056623105131 + [java] + [java] Testing alignment doubling: [java] seq1: 6 4 [java] seq2: 6 4 [java] seq3: 6 4 @@ -2843,15 +2991,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2866,8 +3005,6 @@ [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2881,33 +3018,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] 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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] human: 768 4 @@ -2921,7 +3031,7 @@ [java] 768 sites [java] 69 patterns [java] - [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -2935,7 +3045,7 @@ [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 ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic @@ -2948,7 +3058,7 @@ [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 @@ -2963,6 +3073,22 @@ [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [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_SINGLE COMPUTATION_SYNCH SCALING_MANUAL @@ -2986,6 +3112,19 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== @@ -3001,6 +3140,19 @@ [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] German_ST: 8 2 [java] Dutch_List: 8 2 [java] English_ST: 8 2 @@ -3030,6 +3182,19 @@ [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] German_ST: 5051 4 + [java] Dutch_List: 5051 4 + [java] English_ST: 5051 4 + [java] French: 5051 4 + [java] Italian: 5051 4 + [java] Spanish: 5051 4 + [java] Stripping invariant sites + [java] <0> <1> removed 4486 sites + [java] Alignment(null) + [java] 6 taxa + [java] 5051 sites with weight 565 + [java] 50 patterns + [java] [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3037,11 +3202,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [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 69 unique site patterns. + [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -3050,21 +3215,8 @@ [java] ============================================================================================================== [java] Ignoring 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] German_ST: 5051 4 - [java] Dutch_List: 5051 4 - [java] English_ST: 5051 4 - [java] French: 5051 4 - [java] Italian: 5051 4 - [java] Spanish: 5051 4 - [java] Stripping invariant sites - [java] <0> <1> removed 4486 sites - [java] Alignment(null) - [java] 6 taxa - [java] 5051 sites with weight 565 - [java] 50 patterns - [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3080,9 +3232,14 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Using ambiguities in tree likelihood. + [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] With 32 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -3091,7 +3248,11 @@ [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] 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] ============================================================================================================== @@ -3125,28 +3286,6 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3171,24 +3310,6 @@ [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 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] @@ -3202,17 +3323,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] - [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: EIGEN_COMPLEX [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3231,6 +3341,26 @@ [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] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] + [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: EIGEN_COMPLEX [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 @@ -3251,6 +3381,19 @@ [java] 85 sites [java] 32 patterns [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] =============================================================================== + [java] Citations for this model: + [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. == @@ -3260,113 +3403,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [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) - [java] at beast.base.core.BEASTInterface.validateInputs(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.operator.DeltaExchangeOperatorTest.testCanOperate(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] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX - [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, @@ -3378,7 +3414,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -14.297530455869882 - [java] End likelihood: -2.101581781210349 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 @@ -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: 6.9 seconds + [java] Total calculation time: 3.421 seconds + [java] End likelihood: -2.101581781210349 [java] =============================================================================== [java] Citations for this model: [java] @@ -3404,7 +3440,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -7.148765227934941 - [java] End likelihood: 0.008929267909451477 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.31053 307447 692554 1.00000 0.30745 @@ -3416,7 +3451,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.664 seconds + [java] Total calculation time: 2.841 seconds + [java] End likelihood: 0.008929267909451477 [java] =============================================================================== [java] Citations for this model: [java] @@ -3443,7 +3479,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.924 seconds + [java] Total calculation time: 3.302 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3457,6 +3493,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 + [java] End likelihood: -2.422052674651341 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -3468,8 +3505,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.993 seconds - [java] End likelihood: -2.422052674651341 + [java] Total calculation time: 5.343 seconds [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3516,7 +3552,6 @@ [java] [java] =============================================================================== [java] Start likelihood: 0.6286086594223761 - [java] End likelihood: 3.119201359019653 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(unknown) 0.46265 69697 930304 1.00000 0.06970 Try setting delta to about 0.231 @@ -3528,7 +3563,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.002 seconds + [java] Total calculation time: 2.905 seconds + [java] End likelihood: 3.119201359019653 [java] Testing mirror distribution [java] Testing mirror distribution for scaling [java] kick in @@ -3557,232 +3593,6 @@ [java] Testing bactrian_triangle s= 0.999423750532334 [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 - [java] Testing bactrian_box s= 0.9993638943013682 - [java] Number of weights (4) does not match sequence length (16) - [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] - [java] 0human AAAACCCCGGGGTTTT - [java] 1chimp ACGTACGTACGTACGT - [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] - [java] AAAACCCCTTTTGGGG - [java] ACTGACGTACGTACGT - [java] [101000, 10000, 1, 110] - [java] GGGAAA - [java] AGGACA - [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. - [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] - [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] - [java] <0> <1> <2> <3> removed 6 sites - [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] - [java] t0=0 - [java] t1=10 - [java] t1=10 - [java] WARNING: no trait specified for t0: Assumed to be 10.0 - [java] t0=0 - [java] t1=10 [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -4036,6 +3846,232 @@ [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] + [java] 0human AAAACCCCGGGGTTTT + [java] 1chimp ACGTACGTACGTACGT + [java] [11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] AAAACCCCTTTTGGGG + [java] ACTGACGTACGTACGT + [java] [101000, 10000, 1, 110] + [java] GGGAAA + [java] AGGACA + [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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] initAndValidate() failed! Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] java.lang.IllegalArgumentException: constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testConstantSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) + [java] at java.base/java.lang.reflect.Method.invoke(Method.java:568) + [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java: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] initAndValidate() failed! constantSiteWeights should be of the same dimension as the datatype (3!=4) + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 1, 1, 4, 1, 1, 1, 1, 5] + [java] [11233, 1, 1, 1, 1, 3, 1, 1, 3, 4] + [java] <0> <1> <2> <3> removed 6 sites + [java] [11232, 1, 1, 1, 1, 2, 1, 1, 3, 4] + [java] t0=0 + [java] t1=10 + [java] t1=10 + [java] WARNING: no trait specified for t0: Assumed to be 10.0 + [java] t0=0 + [java] t1=10 [java] Distribution lower = 0, upper = 6 windowSize = 1 Average deviation: 2957 [java] Distribution lower = 0, upper = 6 windowSize = 2 Average deviation: 2179 [java] Distribution lower = 0, upper = 6 windowSize = 3 Average deviation: 3318 @@ -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: 8.872 seconds + [java] Total calculation time: 4.733 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: 4.75 seconds + [java] Total calculation time: 4.919 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 @@ -4114,20 +4150,6 @@ [java] [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.8084620917497215 - [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] 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] 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] 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] 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] @@ -4152,6 +4174,20 @@ [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] 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] 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] 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] 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] Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [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: 20.873 seconds + [java] Total calculation time: 17.431 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438963848 variance: 1.6815511765072393 ESS: 106131.3927120149 @@ -4225,10 +4261,6 @@ [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] - [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] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [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] @@ -4253,7 +4285,10 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] 9.094947017729282E-13 + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -4280,7 +4315,7 @@ [java] 6 taxa [java] 5051 sites [java] 50 patterns - [java] + [java] 9.094947017729282E-13 [java] Starting frequencies: [1.0, 0.0] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [6, 50, 5051] @@ -4333,6 +4368,7 @@ [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 + [java] [java] gorilla: 768 4 [java] orangutan: 768 4 [java] siamang: 768 4 @@ -15259,7 +15295,6 @@ [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] 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) @@ -15367,16 +15402,13 @@ [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 ✔ @@ -15394,10 +15426,6 @@ [java] │ ├─ BEASTInterfaceTest ✔ [java] │ │ ├─ testInputType() ✔ [java] │ │ └─ testBEASTi() ✔ - [java] │ ├─ LoggerTest ✔ - [java] │ │ ├─ testFileLog() ✔ - [java] │ │ ├─ testScreenLog() ✔ - [java] │ │ └─ isLoggingToStdout() ✔ [java] │ ├─ InputForAnnotatedConstructorTest ✔ [java] │ │ ├─ testEnumerationInput() ✔ [java] │ │ ├─ testArrayInput() ✔ @@ -15408,13 +15436,17 @@ [java] │ │ ├─ testJSON() ✔ [java] │ │ ├─ testInnerClass() ✔ [java] │ │ └─ testPrimitiveInput() ✔ + [java] │ ├─ LoggerTest ✔ + [java] │ │ ├─ testFileLog() ✔ + [java] │ │ ├─ testScreenLog() ✔ + [java] │ │ └─ isLoggingToStdout() ✔ + [java] │ ├─ BooleanParameterListTest ✔ + [java] │ │ └─ test1() ✔ [java] │ ├─ InputTest ✔ [java] │ │ ├─ testOptionalInput() ✔ [java] │ │ ├─ testScientificNotationDecimalFailure() ✔ [java] │ │ ├─ testScienticNotation() ✔ [java] │ │ └─ testScientificNotationIntTooLarge() ✔ - [java] │ ├─ BooleanParameterListTest ✔ - [java] │ │ └─ test1() ✔ [java] │ ├─ IntegerParameterListTest ✔ [java] │ │ └─ test1() ✔ [java] │ ├─ OperatorScheduleTest ✔ @@ -15430,16 +15462,24 @@ [java] │ │ └─ testSum() ✔ [java] │ ├─ UncertainAlignmentTest ✔ [java] │ │ └─ testUncertainAlignment() ✔ + [java] │ ├─ BactrianIntervalOperatorTest ✔ + [java] │ │ ├─ testLogNormalDistribution() 12247 ms ✔ + [java] │ │ ├─ testNormalDistribution() 11820 ms ✔ + [java] │ │ ├─ testUniformDistributionZeroUpperBound() 11134 ms ✔ + [java] │ │ ├─ testUniformDistribution() 11642 ms ✔ + [java] │ │ └─ testUniformDistributionZeroLowerBound() 11549 ms ✔ [java] │ ├─ DataTypeDeEncodeTest ✔ [java] │ │ └─ testDataTypeDeEncode() ✔ - [java] │ ├─ BactrianIntervalOperatorTest ✔ - [java] │ │ ├─ testLogNormalDistribution() 23142 ms ✔ - [java] │ │ ├─ testNormalDistribution() 21313 ms ✔ - [java] │ │ ├─ testUniformDistributionZeroUpperBound() 19451 ms ✔ - [java] │ │ ├─ testUniformDistribution() 19346 ms ✔ - [java] │ │ └─ testUniformDistributionZeroLowerBound() 19272 ms ✔ + [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] │ ├─ GeneralSubstitutionModelTest ✔ [java] │ │ └─ getTransitionProbabilities() ✔ + [java] │ ├─ DeltaExchangeOperatorTest ✔ + [java] │ │ ├─ testKeepsSum() ✔ + [java] │ │ ├─ testCanOperate() ✔ + [java] │ │ └─ testKeepsWeightedSum() ✔ [java] │ ├─ BeagleTreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15476,10 +15516,6 @@ [java] │ │ ├─ testAminoAcidLikelihoodcpRev() ✔ [java] │ │ ├─ testAminoAcidLikelihoodBlosum62() ✔ [java] │ │ └─ testAminoAcidLikelihoodGIDayhoff() ✔ - [java] │ ├─ DeltaExchangeOperatorTest ✔ - [java] │ │ ├─ testKeepsSum() ✔ - [java] │ │ ├─ testCanOperate() ✔ - [java] │ │ └─ testKeepsWeightedSum() ✔ [java] │ ├─ BactrianScaleOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testTwoDimensionalDistribution() ✔ @@ -15488,19 +15524,19 @@ [java] │ │ ├─ testScaleAllIndependentlylDistribution() ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() 29550 ms ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() 21943 ms ✔ - [java] │ │ └─ testNarrowExchange6Taxa() 21814 ms ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() 13517 ms ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() 13490 ms ✔ + [java] │ │ └─ testNarrowExchange6Taxa() 12916 ms ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ [java] │ │ ├─ testKeepsSum() ✔ [java] │ │ ├─ testCanOperate() ✔ [java] │ │ └─ testKeepsWeightedSum() ✔ - [java] │ ├─ YuleModelTest ✔ - [java] │ │ └─ testYule() ✔ [java] │ ├─ ScaleOperatorTest ✔ [java] │ │ └─ testTreeScaling() ✔ + [java] │ ├─ YuleModelTest ✔ + [java] │ │ └─ testYule() ✔ [java] │ ├─ NodeTest ✔ [java] │ │ ├─ testToNewick() ✔ [java] │ │ ├─ testRootToString() ✔ @@ -15510,7 +15546,7 @@ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistribution() ✔ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistributionScaler() ✔ [java] │ │ ├─ testMirrorfKernelDistribution() ✔ - [java] │ │ └─ testBactrianKernelDistribution() ✔ + [java] │ │ └─ testBactrianKernelDistribution() 20776 ms ✔ [java] │ ├─ FilteredAlignmentTest ✔ [java] │ │ ├─ testWeightedSites() ✔ [java] │ │ ├─ testFilteredFileredAlignment() ✔ @@ -15526,17 +15562,17 @@ [java] │ ├─ TreeTest ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x6() 14845 ms ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() 38806 ms ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() 69664 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x6() 23494 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() 41129 ms ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() 41484 ms ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() 25800 ms ✔ - [java] │ │ └─ testLogNormalDistribution() 23362 ms ✔ + [java] │ │ ├─ testNormalDistribution() 13521 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 13763 ms ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 56954 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 39708 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15580,7 +15616,7 @@ [java] │ ├─ CompoundParameterHelperTest ✔ [java] │ │ └─ testCompoundParameterHelper() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 76656 ms ✔ + [java] │ │ └─ testCoalescentTimes() 45760 ms ✔ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ @@ -15591,11 +15627,11 @@ [java] │ │ ├─ testCDFAndQuantile() ✔ [java] │ │ ├─ testLogPdf() ✔ [java] │ │ └─ testMedian() ✔ - [java] │ ├─ GammaTest ✔ - [java] │ │ └─ testGammaCummulative() ✔ [java] │ ├─ MRCAPriorTest ✔ [java] │ │ ├─ testMRCATimePrior() ✔ [java] │ │ └─ testSingleMonophyleticConstraint() ✔ + [java] │ ├─ GammaTest ✔ + [java] │ │ └─ testGammaCummulative() ✔ [java] │ ├─ MeanOfParametricDistributionTest ✔ [java] │ │ ├─ testMeanOfExponential() ✔ [java] │ │ ├─ testMeanOfUniform() ✔ @@ -15639,7 +15675,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 547521 ms + [java] Test run finished after 375266 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/null46148543 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1242427548 [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: 3593ms -[junitreport] Deleting: /tmp/null46148543 +[junitreport] Transform time: 2219ms +[junitreport] Deleting: /tmp/null1242427548 junit-integration: [java] @@ -15676,23 +15712,19 @@ [java] [java] [java] - [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 ✔ [java] │ ├─ InputTypeTest ✔ [java] │ │ ├─ testInputTypeCanBeSet() ✔ [java] │ │ └─ testAnnotatedInputHasGetters() ✔ - [java] │ ├─ XMLElementNameTest ✔ - [java] │ │ ├─ test_ReservedElementNames() ✔ - [java] │ │ └─ test_NameUniqueness() ✔ [java] │ ├─ DocumentationTest ✔ [java] │ │ ├─ testDescriptions() ✔ [java] │ │ ├─ test_DocMaker() ✔ [java] │ │ └─ testInputTipText() ✔ + [java] │ ├─ XMLElementNameTest ✔ + [java] │ │ ├─ test_ReservedElementNames() ✔ + [java] │ │ └─ test_NameUniqueness() ✔ [java] │ ├─ XMLProducerTest ✔ [java] │ │ ├─ test_ThatNexusExamplesProduces() ✔ [java] │ │ └─ testObjectWithoutID() ✔ @@ -15700,7 +15732,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 4409 ms + [java] Test run finished after 3407 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15714,15 +15746,21 @@ [java] [ 9 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null2055670172 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null885130022 [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: 1475ms -[junitreport] Deleting: /tmp/null2055670172 +[junitreport] Transform time: 1243ms +[junitreport] Deleting: /tmp/null885130022 junit-xmlparsertest: [java] [java] Thanks for using JUnit! Support its development at https://junit.org/sponsoring [java] + [java] + [java] WARNING: Delegated to the 'execute' command. [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ @@ -15730,7 +15768,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1998 ms + [java] Test run finished after 1152 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15740,23 +15778,21 @@ [java] [ 1 tests found ] [java] [ 0 tests skipped ] [java] [ 1 tests started ] - [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] [ 0 tests aborted ] [java] [ 1 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null52340694 + [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/null1164308685 [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: 748ms -[junitreport] Deleting: /tmp/null52340694 +[junitreport] Transform time: 317ms +[junitreport] Deleting: /tmp/null1164308685 junit: BUILD SUCCESSFUL -Total time: 9 minutes 35 seconds +Total time: 6 minutes 33 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15785,8 +15821,8 @@ dpkg-gencontrol: warning: Depends field of package beast2-mcmc-examples: substitution variable ${shlibs:Depends} used, but is not defined dh_md5sums dh_builddeb -dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.6+dfsg-1_all.deb'. dpkg-deb: building package 'beast2-mcmc-examples' in '../beast2-mcmc-examples_2.7.6+dfsg-1_all.deb'. +dpkg-deb: building package 'beast2-mcmc' in '../beast2-mcmc_2.7.6+dfsg-1_all.deb'. dpkg-genbuildinfo --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_armhf.buildinfo dpkg-genchanges --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -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/498/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/498/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/3576 and its subdirectories -I: Current time: Thu Apr 11 10:45:52 -12 2024 -I: pbuilder-time-stamp: 1712875552 +I: removing directory /srv/workspace/pbuilder/498 and its subdirectories +I: Current time: Fri Apr 12 12:57:33 +14 2024 +I: pbuilder-time-stamp: 1712876253