Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 05:45:11.483298523 +0000 +++ b2/build.log 2024-05-07 05:48:40.458402742 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 6 17:24:48 -12 2024 -I: pbuilder-time-stamp: 1715059488 +I: Current time: Tue Jun 10 02:08:15 +14 2025 +I: pbuilder-time-stamp: 1749470895 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/875119/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2428908/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 9 12:08 /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/2428908/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2428908/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=20 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='e2f4a19dc8844d13850226c19496eaac' - 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='875119' - PS1='# ' - PS2='> ' + INVOCATION_ID=68534d18e9124fa3b9eb5da87e12ff3a + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2428908 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.2RkWy7d9/pbuilderrc_XsyF --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.2RkWy7d9/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.2RkWy7d9/pbuilderrc_GVlw --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.2RkWy7d9/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos11-amd64 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 3 08:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/875119/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 7 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2428908/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -468,7 +500,7 @@ Get: 319 http://deb.debian.org/debian trixie/main amd64 libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 320 http://deb.debian.org/debian trixie/main amd64 libopenjfx-jni amd64 11.0.11+1-3.2 [22.2 MB] Get: 321 http://deb.debian.org/debian trixie/main amd64 libopenjfx-java all 11.0.11+1-3.2 [8903 kB] -Fetched 354 MB in 16s (22.0 MB/s) +Fetched 354 MB in 4s (85.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19698 files and directories currently installed.) @@ -1531,8 +1563,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue May 7 05:31:14 UTC 2024. -Universal Time is now: Tue May 7 05:31:14 UTC 2024. +Local time is now: Mon Jun 9 12:09:19 UTC 2025. +Universal Time is now: Mon Jun 9 12:09:19 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1990,7 +2022,11 @@ 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/2428908/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2428908/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 @@ -2006,7 +2042,7 @@ clean: BUILD SUCCESSFUL -Total time: 2 seconds +Total time: 0 seconds jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' @@ -2109,7 +2145,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 2 minutes 23 seconds +Total time: 16 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' @@ -2143,14 +2179,6 @@ [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$BEASTi (id null): [java] Writing file beast.log [java] Sample null.1 null.2 [java] 1 0.3 0.7 -- @@ -2160,38 +2188,18 @@ [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } [java] ] [java] } + [java] OK + [java] test getCitation + [java] test initByName + [java] test listInputs + [java] test initByName + [java] test getInputValue + [java] test getOutputs + [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): [java] 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. [java] Operator weighting may not work as expected. - [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] Tip likelihoods: - [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 0.0 0.0 1.0 ; - [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 1.0 0.0 0.0 ; - [java] 0.4 0.0 0.6 0.0 ; 0.0 0.6 0.0 0.4 ; 0.0 1.0 0.0 0.0 ; - [java] Most likely sequences: - [java] ATT - [java] ATC - [java] GCC - [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] =============================================================================== [java] Citations for this model: [java] @@ -2216,7 +2224,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 7.838 seconds + [java] Total calculation time: 0.928 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516753 variance: 1.7216547315139537 ESS: 25717.88066361133 @@ -2248,14 +2256,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 7.203 seconds + [java] Total calculation time: 1.001 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326598056 variance: 0.00998468201961599 ESS: 199303.5697419037 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: 1.3580153849811107 + [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -2280,14 +2288,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.901 seconds + [java] Total calculation time: 0.915 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712321 variance: 0.33333524355318095 ESS: 198672.26933150744 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.6931471805599453 + [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -2312,7 +2320,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 9.022 seconds + [java] Total calculation time: 0.882 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.0000858829347083 variance: 0.3333352435532249 ESS: 198672.2693314681 @@ -2344,7 +2352,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.978 seconds + [java] Total calculation time: 0.889 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834570785 variance: 0.3333352435537157 ESS: 198672.26933227608 @@ -2352,6 +2360,34 @@ [java] [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log + [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] Tip likelihoods: + [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 0.0 0.0 1.0 ; + [java] 0.7 0.0 0.3 0.0 ; 0.0 0.3 0.0 0.7 ; 0.0 1.0 0.0 0.0 ; + [java] 0.4 0.0 0.6 0.0 ; 0.0 0.6 0.0 0.4 ; 0.0 1.0 0.0 0.0 ; + [java] Most likely sequences: + [java] ATT + [java] ATC + [java] GCC + [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] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] [java] freqs = [java] [0.3333333, 0.3333333, 0.3333333] @@ -2379,29 +2415,118 @@ [java] 85 sites [java] 32 patterns [java] + [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] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [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] 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. @@ -2415,28 +2540,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [java] 69 patterns - [java] - [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2459,6 +2562,96 @@ [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] 6.821210263296962E-13 + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [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_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 [java] Alignment(null) [java] 3 taxa [java] 85 sites @@ -2466,11 +2659,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== [java] 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 @@ -2482,10 +2670,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2497,20 +2681,6 @@ [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] 6.821210263296962E-13 - [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: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU @@ -2531,28 +2701,6 @@ [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_COMPLEX SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] [java] Struthio_camelus: 85 20 @@ -2565,15 +2713,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] 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 @@ -2585,15 +2724,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -2614,15 +2744,6 @@ [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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 768 4 @@ -2636,24 +2757,6 @@ [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] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -2685,14 +2788,42 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [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] ============================================================================================================== + [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] ============================================================================================================== + [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. @@ -2710,38 +2841,6 @@ [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] 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_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -11.85320233632878 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -11.85320233632878 - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -11.85320233632878 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -12.069603116476458 - [java] - [java] Tree B: [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2768,44 +2867,6 @@ [java] Using character uncertainty in tree likelihood. [java] With 3 unique site patterns. [java] Using rescaling scheme : none - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -12.421114302827698 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -12.421114302827698 - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -12.421114302827698 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -11.621056623105131 - [java] - [java] Testing alignment doubling: - [java] seq1: 6 4 - [java] seq2: 6 4 - [java] seq3: 6 4 - [java] Alignment(null) - [java] 3 taxa - [java] 6 sites - [java] 6 patterns - [java] - [java] Most probable sequences: - [java] ATTATT - [java] ATCATC - [java] GCCGCC - [java] Without tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -24.8422286056554 - [java] With tip likelihoods: - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] -23.242113246210263 [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2845,23 +2906,6 @@ [java] Using character uncertainty in tree likelihood. [java] With 6 unique site patterns. [java] Using rescaling scheme : none - [java] German_ST: 64 4 - [java] Dutch_List: 64 4 - [java] English_ST: 64 4 - [java] Alignment(null) - [java] 3 taxa - [java] 64 sites - [java] 64 patterns - [java] - [java] Starting frequencies: [0.2, 0.3, 0.4, 0.1] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2880,33 +2924,10 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [java] ============================================================================================================== - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [java] 69 patterns - [java] [java] 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: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2920,22 +2941,6 @@ [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_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2958,6 +2963,290 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 8 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 8 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 69 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] 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] + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] ============================================================================================================== + [java] + [java] -11.85320233632878 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] ============================================================================================================== with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Ignoring ambiguities in tree likelihood. + [java] + [java] -11.85320233632878 + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU============================================================================================================== + [java] -11.85320233632878 + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU== Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] + [java] ==============================================================================================================-12.069603116476458 + [java] ============================================================================================================== + [java] + [java] + [java] Tree B: + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] Ignoring ambiguities in tree likelihood. with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] + [java] Using rescaling scheme : dynamic-12.421114302827698 + [java] + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] ============================================================================================================== with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] ============================================================================================================== + [java] + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. ==-12.421114302827698 + [java] + [java] Without tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] ============================================================================================================== with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] + [java] -12.421114302827698 + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] With tip likelihoods: Ignoring character uncertainty in tree likelihood. + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU============================================================================================================== + [java] -11.621056623105131 + [java] + [java] + [java] Testing alignment doubling:== Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] seq1: 6 4 + [java] seq2: 6 4 + [java] seq3: 6 4 + [java] Alignment(null) + [java] 3 taxa + [java] 6 sites + [java] 6 patterns + [java] + [java] Most probable sequences: + [java] ATTATT + [java] ATCATC + [java] GCCGCC + [java] + [java] Without tip likelihoods:============================================================================================================== + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] + [java] ============================================================================================================== with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] + [java] -24.8422286056554 + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] With tip likelihoods: + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] -23.242113246210263 + [java] German_ST: 64 4 + [java] Dutch_List: 64 4 + [java] English_ST: 64 4 + [java] Alignment(null) + [java] 3 taxa + [java] 64 sites + [java] 64 patterns + [java] + [java] Starting frequencies: [0.2, 0.3, 0.4, 0.1] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Starting frequencies: [0.087, 0.033, 0.047, 0.05, 0.04, 0.089, 0.034, 0.037, 0.08, 0.085, 0.015, 0.04, 0.051, 0.038, 0.041, 0.07, 0.058, 0.065, 0.01, 0.03] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2986,37 +3275,11 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] 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 BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] - [java] ============================================================================================================== - [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] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -3036,19 +3299,6 @@ [java] 8 patterns [java] [java] Starting frequencies: [0.683, 0.317] - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 8 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 8 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3067,19 +3317,6 @@ [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_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 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_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] German_ST: 5051 4 @@ -3095,19 +3332,6 @@ [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. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 50 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3123,24 +3347,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 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 @@ -3164,19 +3370,6 @@ [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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3193,24 +3386,6 @@ [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [java] Starting frequencies: [0.0866, 0.0193, 0.057, 0.0581, 0.0384, 0.0833, 0.0244, 0.0485, 0.062, 0.0862, 0.0195, 0.0391, 0.0458, 0.0367, 0.044, 0.0695, 0.061, 0.0709, 0.0144, 0.0353] - [java] ============================================================================================================== - [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] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -3230,15 +3405,6 @@ [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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU [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] @@ -3252,15 +3418,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] 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 @@ -3283,85 +3440,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE COMPUTATION_SYNCH EIGEN_REAL SCALING_MANUAL SCALERS_RAW VECTOR_SSE THREADING_NONE PROCESSOR_CPU FRAMEWORK_CPU - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 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$9(NodeTestTask.java:139) - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.execute(NodeTestTask.java:95) - [java] at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.submit(SameThreadHierarchicalTestExecutorService.java:35) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestExecutor.execute(HierarchicalTestExecutor.java:57) - [java] at org.junit.platform.engine.support.hierarchical.HierarchicalTestEngine.execute(HierarchicalTestEngine.java:54) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:198) [java] =============================================================================== [java] Citations for this model: [java] @@ -3375,48 +3453,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -14.297530455869882 - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:169) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.execute(EngineExecutionOrchestrator.java:93) - [java] at org.junit.platform.launcher.core.EngineExecutionOrchestrator.lambda$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] End likelihood: -2.1015817812114337 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.30772 308831 691170 1.00000 0.30883 @@ -3428,8 +3465,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 5.896 seconds - [java] End likelihood: -2.1015817812114337 + [java] Total calculation time: 0.59 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3455,7 +3491,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.432 seconds + [java] Total calculation time: 0.467 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3469,7 +3505,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 - [java] End likelihood: -0.5552616722750887 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.33125 153295 347047 0.50000 0.30638 @@ -3482,7 +3517,8 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.875 seconds + [java] Total calculation time: 0.73 seconds + [java] End likelihood: -0.5552616722750887 [java] =============================================================================== [java] Citations for this model: [java] @@ -3507,7 +3543,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 9.552 seconds + [java] Total calculation time: 0.87 seconds [java] End likelihood: -2.422052674650429 [java] A: 1 4 [java] B: 1 4 @@ -3556,6 +3592,7 @@ [java] =============================================================================== [java] Start likelihood: 0.6286086594223761 [java] End likelihood: 3.1192013590196357 + [java] Testing mirror distribution [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianDeltaExchangeOperator(unknown) 0.46265 69697 930304 1.00000 0.06970 Try setting delta to about 0.231 @@ -3567,8 +3604,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.606 seconds - [java] Testing mirror distribution + [java] Total calculation time: 0.479 seconds [java] Testing mirror distribution for scaling [java] kick in [java] kick in @@ -3596,69 +3632,6 @@ [java] Testing bactrian_triangle s= 0.999423750532334 [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites with weight 12514 - [java] 16 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites with weight 12514 - [java] 16 patterns - [java] - [java] 0human: 6 4 - [java] 1chimp: 6 4 - [java] Alignment(null) - [java] 2 taxa - [java] 6 sites - [java] 4 patterns - [java] - [java] 0human: 6 4 - [java] 1chimp: 6 4 - [java] Alignment(null) - [java] 2 taxa - [java] 6 sites with weight 111111 - [java] 4 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites with weight 12514 - [java] 16 patterns - [java] [java] Testing bactrian_box s= 0.9993638943013682 [java] Number of weights (4) does not match sequence length (16) [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] @@ -3809,7 +3782,7 @@ [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] 0human: 16 4 at org.junit.platform.engine.support.hierarchical.SameThreadHierarchicalTestExecutorService.invokeAll(SameThreadHierarchicalTestExecutorService.java:41) + [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) @@ -3885,7 +3858,70 @@ [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) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites with weight 12514 + [java] 16 patterns + [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites with weight 12514 + [java] 16 patterns + [java] + [java] 0human: 6 4 + [java] 1chimp: 6 4 + [java] Alignment(null) + [java] 2 taxa + [java] 6 sites + [java] 4 patterns + [java] + [java] 0human: 6 4 + [java] 1chimp: 6 4 + [java] Alignment(null) + [java] 2 taxa + [java] 6 sites with weight 111111 + [java] 4 patterns [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites with weight 12514 + [java] 16 patterns + [java] + [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa @@ -4113,7 +4149,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.912 seconds + [java] Total calculation time: 0.745 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873339 variance: 0.9962228119352623 ESS: 194315.96975230493 @@ -4145,14 +4181,30 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 1.393 seconds + [java] Total calculation time: 0.792 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516753 variance: 1.7216547315139537 ESS: 25717.88066361133 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.8084620917494391 + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] + [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] + [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] + [java] trace log written to /tmp/bactrian.log [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4188,22 +4240,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -6.753673320834167 - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] - [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.1584087537031632, 0.01389998976971136, 0.7609221549346824, 0.06676910159244315] - [java] Calculat: [0.15840875370312343, 0.013899989769708488, 0.7609221549344917, 0.06676910159242638, 0.1584087537031232, 0.013899989769708469, 0.7609221549344906, 0.0667691015924263, 0.15840875370312313, 0.01389998976970846, 0.7609221549344901, 0.06676910159242626, 0.15840875370312307, 0.013899989769708455, 0.7609221549344899, 0.06676910159242623] [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] beast.base.inference.operator.kernel.BactrianUpDownOperator(unknown) 0.02500 435934 2062466 0.50000 0.17449 @@ -4217,14 +4253,19 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 11.419 seconds + [java] Total calculation time: 3.303 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438964741 variance: 1.681551176507236 ESS: 106131.39271214437 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.20113760214313903 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.20113760214313903 + [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] 1.1368683772161603E-12 [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 @@ -4236,10 +4277,6 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. - [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -4308,7 +4345,6 @@ [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] - [java] 1.1368683772161603E-12 [java] German_ST: 5051 2 [java] Dutch_List: 5051 2 [java] English_ST: 5051 2 @@ -4541,6 +4577,16 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] t 0=0 + [java] t 1=1 + [java] t 2=2 + [java] t 3=3 + [java] t 4=4 + [java] t 5=5 + [java] t 6=6 + [java] t 7=7 + [java] t 8=8 + [java] t 9=9 [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 @@ -4768,16 +4814,6 @@ [java] t 7 = 7 (7.0) [java] t 8 = 8 (8.0) [java] t 9 = 9 (9.0) - [java] t 0=0 - [java] t 1=1 - [java] t 2=2 - [java] t 3=3 - [java] t 4=4 - [java] t 5=5 - [java] t 6=6 - [java] t 7=7 - [java] t 8=8 - [java] t 9=9 [java] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -14759,63 +14795,6 @@ [java] Testing logNormal[M=-0.9229165374565262 S=1.4755430483683152].pdf(1.8753310361541204) [java] Testing logNormal[M=3.1022135031859257 S=7.702390036376917].pdf(2.0958333470463852) [java] Testing logNormal[M=-3.2285375769560454 S=5.8518018730607215].pdf(2.1529570547929944) - [java] Testing logNormal[M=4.393236740609151 S=6.479253711666502].pdf(1.5637780165482158) - [java] Testing logNormal[M=3.7762794609295476 S=1.024111399230745].pdf(2.094700778040578) - [java] Testing logNormal[M=1.0510857736096852 S=6.56884992113222].pdf(0.9694984036752307) - [java] Testing logNormal[M=-2.4461641507945355 S=9.053173443013412].pdf(0.44401026031478447) - [java] Testing logNormal[M=-3.3305859424334603 S=4.665798611302337].pdf(0.5350124694365618) - [java] Testing logNormal[M=3.0154300969764645 S=2.207022774317775].pdf(0.8338564593532116) - [java] Testing logNormal[M=4.951757346938939 S=0.4847578051229251].pdf(1.8879879495120273) - [java] Testing logNormal[M=1.4396936072648083 S=0.9352375529227908].pdf(0.4095152803562465) - [java] Testing logNormal[M=-0.4671469545995235 S=9.789762938061312].pdf(2.2455880527911005) - [java] Testing logNormal[M=-1.5088998442508537 S=6.471017582561861].pdf(2.0612864160084907) - [java] Testing logNormal[M=4.991789312878806 S=6.554345293674297].pdf(0.5584142661362375) - [java] Testing logNormal[M=-3.5199399616382565 S=7.375809697312937].pdf(2.1925210408637557) - [java] Testing logNormal[M=3.6305897605016373 S=4.447733872601773].pdf(2.114657921637381) - [java] Testing logNormal[M=-4.774063073881706 S=1.569379307371782].pdf(0.4672215131828263) - [java] Testing logNormal[M=2.4100054620822933 S=8.551369286249571].pdf(1.9966101452559766) - [java] Testing logNormal[M=-2.174624381910877 S=4.261976707939943].pdf(1.3893844287443138) - [java] Testing logNormal[M=2.4474163247561975 S=9.0687518244901].pdf(1.0584465112030501) - [java] Testing logNormal[M=-4.0876388610026915 S=2.3580155263010285].pdf(2.174557298861372) - [java] Testing logNormal[M=4.178076363061082 S=7.652050341912081].pdf(1.8064484123176598) - [java] Testing logNormal[M=-4.2942511361821625 S=7.90706205554277].pdf(0.9008073642621347) - [java] Testing logNormal[M=-3.400521933469606 S=1.2676996814990704].pdf(1.9341739529998083) - [java] Testing logNormal[M=3.227885602221974 S=0.44254009760756774].pdf(1.9246707295109748) - [java] Testing logNormal[M=-1.9546778392000688 S=5.371917139147316].pdf(1.513048181913233) - [java] Testing logNormal[M=-3.905965186925191 S=9.382531249150695].pdf(2.1849985291906915) - [java] Testing logNormal[M=-3.8815720763834385 S=2.7391098866153065].pdf(2.116831044985781) - [java] Testing logNormal[M=-2.006576079672752 S=3.384742653428426].pdf(0.1772130943572065) - [java] Testing logNormal[M=0.7739731577623044 S=1.9290685109678585].pdf(2.133555461509354) - [java] Testing logNormal[M=2.899591920716115 S=2.757991426916332].pdf(2.1200243263834295) - [java] Testing logNormal[M=4.532523286888125 S=5.126204743674573].pdf(1.7593769511936672) - [java] Testing logNormal[M=-0.49888733180977063 S=8.831637506022973].pdf(2.0195276977650893) - [java] Testing logNormal[M=1.7882465913011085 S=1.298561562253927].pdf(1.6253669850686407) - [java] Testing logNormal[M=-2.1255375797371623 S=0.20213462984972508].pdf(0.5711484423304036) - [java] Testing logNormal[M=1.1114319979118905 S=3.848986278595966].pdf(2.1337512420532665) - [java] Testing logNormal[M=1.845381991031899 S=0.855275919539259].pdf(2.251802468549937) - [java] Testing logNormal[M=-2.1685664664566993 S=7.501024107148834].pdf(2.2153934098481765) - [java] Testing logNormal[M=0.49292138787465856 S=3.800446106023554].pdf(1.7059270627263858) - [java] Testing logNormal[M=-2.6926168779727377 S=5.478834691645824].pdf(1.7592123635419519) - [java] Testing logNormal[M=-0.7916595618469096 S=5.239598680283363].pdf(2.17017037118507) - [java] Testing logNormal[M=0.20720706687562362 S=2.6818137248367444].pdf(1.4307885319319027) - [java] Testing logNormal[M=2.3106040002220656 S=7.976508153473366].pdf(1.7613970080778787) - [java] Testing logNormal[M=-3.1775413932290855 S=5.841711051893313].pdf(2.067227584056325) - [java] Testing logNormal[M=2.593941181841835 S=7.690280429284675].pdf(1.3280401562436173) - [java] Testing logNormal[M=0.030305385486638414 S=8.184722220069283].pdf(0.6149645572358153) - [java] Testing logNormal[M=2.235248883364177 S=3.9796194848860456].pdf(1.5229597812000013) - [java] Testing logNormal[M=-4.807044211792036 S=6.13882573223086].pdf(2.133120462750521) - [java] Testing logNormal[M=-2.492571059295372 S=9.315531656299832].pdf(0.7659775575749477) - [java] Testing logNormal[M=-3.7417474604247514 S=7.2872109398725184].pdf(0.07927007814427384) - [java] Testing logNormal[M=1.6444719578541598 S=9.269551669363953].pdf(1.0366032573572275) - [java] Testing logNormal[M=3.8637202854747272 S=3.05240894392919].pdf(1.2190799761279396) - [java] Testing logNormal[M=-3.4603344216550322 S=3.759246776784887].pdf(0.0035318294351175043) - [java] Testing logNormal[M=-2.0539658840733876 S=8.310879946546684].pdf(2.2972167695995123) - [java] Testing logNormal[M=-3.7325180064042462 S=1.3859096116172553].pdf(2.1770857241111505) - [java] Testing logNormal[M=-3.56603567821 S=0.5769885841094025].pdf(1.4736475214810125) - [java] Testing logNormal[M=0.295537123125845 S=2.588677029004769].pdf(1.8007642268226245) - [java] Testing logNormal[M=-2.023496228033016 S=3.9227618715869506].pdf(1.5882725769254962) - [java] Testing logNormal[M=-3.577699957972137 S=9.345578106358118].pdf(2.165879097028796) - [java] Testing logNormal[M=1.0516748055181635 S=5.484242020370206].pdf(1.6803895137128866) [java] Loading package BEAST.app v2.7.6 [java] Loading package BEAST.app v2.7.6 [java] Loading package BEAST.base v2.7.6 @@ -15058,6 +15037,70 @@ [java] at java.base/java.lang.Double.parseDouble(Double.java:651) [java] at java.base/java.lang.Double.(Double.java:733) [java] ... 111 more + [java] Testing logNormal[M=4.393236740609151 S=6.479253711666502].pdf(1.5637780165482158) + [java] Testing logNormal[M=3.7762794609295476 S=1.024111399230745].pdf(2.094700778040578) + [java] Testing logNormal[M=1.0510857736096852 S=6.56884992113222].pdf(0.9694984036752307) + [java] Testing logNormal[M=-2.4461641507945355 S=9.053173443013412].pdf(0.44401026031478447) + [java] Testing logNormal[M=-3.3305859424334603 S=4.665798611302337].pdf(0.5350124694365618) + [java] Testing logNormal[M=3.0154300969764645 S=2.207022774317775].pdf(0.8338564593532116) + [java] Testing logNormal[M=4.951757346938939 S=0.4847578051229251].pdf(1.8879879495120273) + [java] Testing logNormal[M=1.4396936072648083 S=0.9352375529227908].pdf(0.4095152803562465) + [java] Testing logNormal[M=-0.4671469545995235 S=9.789762938061312].pdf(2.2455880527911005) + [java] Testing logNormal[M=-1.5088998442508537 S=6.471017582561861].pdf(2.0612864160084907) + [java] Testing logNormal[M=4.991789312878806 S=6.554345293674297].pdf(0.5584142661362375) + [java] Testing logNormal[M=-3.5199399616382565 S=7.375809697312937].pdf(2.1925210408637557) + [java] Testing logNormal[M=3.6305897605016373 S=4.447733872601773].pdf(2.114657921637381) + [java] Testing logNormal[M=-4.774063073881706 S=1.569379307371782].pdf(0.4672215131828263) + [java] Testing logNormal[M=2.4100054620822933 S=8.551369286249571].pdf(1.9966101452559766) + [java] Testing logNormal[M=-2.174624381910877 S=4.261976707939943].pdf(1.3893844287443138) + [java] Testing logNormal[M=2.4474163247561975 S=9.0687518244901].pdf(1.0584465112030501) + [java] Testing logNormal[M=-4.0876388610026915 S=2.3580155263010285].pdf(2.174557298861372) + [java] Testing logNormal[M=4.178076363061082 S=7.652050341912081].pdf(1.8064484123176598) + [java] Testing logNormal[M=-4.2942511361821625 S=7.90706205554277].pdf(0.9008073642621347) + [java] Testing logNormal[M=-3.400521933469606 S=1.2676996814990704].pdf(1.9341739529998083) + [java] Testing logNormal[M=3.227885602221974 S=0.44254009760756774].pdf(1.9246707295109748) + [java] Testing logNormal[M=-1.9546778392000688 S=5.371917139147316].pdf(1.513048181913233) + [java] Testing logNormal[M=-3.905965186925191 S=9.382531249150695].pdf(2.1849985291906915) + [java] Testing logNormal[M=-3.8815720763834385 S=2.7391098866153065].pdf(2.116831044985781) + [java] Testing logNormal[M=-2.006576079672752 S=3.384742653428426].pdf(0.1772130943572065) + [java] Testing logNormal[M=0.7739731577623044 S=1.9290685109678585].pdf(2.133555461509354) + [java] Testing logNormal[M=2.899591920716115 S=2.757991426916332].pdf(2.1200243263834295) + [java] Testing logNormal[M=4.532523286888125 S=5.126204743674573].pdf(1.7593769511936672) + [java] Testing logNormal[M=-0.49888733180977063 S=8.831637506022973].pdf(2.0195276977650893) + [java] Testing logNormal[M=1.7882465913011085 S=1.298561562253927].pdf(1.6253669850686407) + [java] Testing logNormal[M=-2.1255375797371623 S=0.20213462984972508].pdf(0.5711484423304036) + [java] Testing logNormal[M=1.1114319979118905 S=3.848986278595966].pdf(2.1337512420532665) + [java] Testing logNormal[M=1.845381991031899 S=0.855275919539259].pdf(2.251802468549937) + [java] Testing logNormal[M=-2.1685664664566993 S=7.501024107148834].pdf(2.2153934098481765) + [java] Testing logNormal[M=0.49292138787465856 S=3.800446106023554].pdf(1.7059270627263858) + [java] Testing logNormal[M=-2.6926168779727377 S=5.478834691645824].pdf(1.7592123635419519) + [java] Testing logNormal[M=-0.7916595618469096 S=5.239598680283363].pdf(2.17017037118507) + [java] Testing logNormal[M=0.20720706687562362 S=2.6818137248367444].pdf(1.4307885319319027) + [java] Testing logNormal[M=2.3106040002220656 S=7.976508153473366].pdf(1.7613970080778787) + [java] Testing logNormal[M=-3.1775413932290855 S=5.841711051893313].pdf(2.067227584056325) + [java] Testing logNormal[M=2.593941181841835 S=7.690280429284675].pdf(1.3280401562436173) + [java] Testing logNormal[M=0.030305385486638414 S=8.184722220069283].pdf(0.6149645572358153) + [java] Testing logNormal[M=2.235248883364177 S=3.9796194848860456].pdf(1.5229597812000013) + [java] Testing logNormal[M=-4.807044211792036 S=6.13882573223086].pdf(2.133120462750521) + [java] Testing logNormal[M=-2.492571059295372 S=9.315531656299832].pdf(0.7659775575749477) + [java] Testing logNormal[M=-3.7417474604247514 S=7.2872109398725184].pdf(0.07927007814427384) + [java] Testing logNormal[M=1.6444719578541598 S=9.269551669363953].pdf(1.0366032573572275) + [java] Testing logNormal[M=3.8637202854747272 S=3.05240894392919].pdf(1.2190799761279396) + [java] Testing logNormal[M=-3.4603344216550322 S=3.759246776784887].pdf(0.0035318294351175043) + [java] Testing logNormal[M=-2.0539658840733876 S=8.310879946546684].pdf(2.2972167695995123) + [java] Testing logNormal[M=-3.7325180064042462 S=1.3859096116172553].pdf(2.1770857241111505) + [java] Testing logNormal[M=-3.56603567821 S=0.5769885841094025].pdf(1.4736475214810125) + [java] Testing logNormal[M=0.295537123125845 S=2.588677029004769].pdf(1.8007642268226245) + [java] Testing logNormal[M=-2.023496228033016 S=3.9227618715869506].pdf(1.5882725769254962) + [java] Testing logNormal[M=-3.577699957972137 S=9.345578106358118].pdf(2.165879097028796) + [java] Testing logNormal[M=1.0516748055181635 S=5.484242020370206].pdf(1.6803895137128866) + [java] adfgad + [java] exception thrown + [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) + [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null + [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) @@ -15405,13 +15448,10 @@ [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:57) [java] at org.junit.platform.console.ConsoleLauncher.run(ConsoleLauncher.java:42) [java] at org.junit.platform.console.ConsoleLauncher.main(ConsoleLauncher.java:35) - [java] adfgad - [java] exception thrown - [java] /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus/Primates.nex (No such file or directory) - [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null - [java] (C:10.0,(B:20.0,A:30.0):10.0):0.0 + [java] + [java] WARNING: Delegated to the 'execute' command. + [java] This behaviour has been deprecated and will be removed in a future release. + [java] Please use the 'execute' command directly. [java] ╷ [java] ├─ JUnit Platform Suite ✔ [java] ├─ JUnit Jupiter ✔ @@ -15426,9 +15466,6 @@ [java] │ │ ├─ testGetKey() ✔ [java] │ │ ├─ testParamter() ✔ [java] │ │ └─ testKeysTwoColumns() ✔ - [java] │ ├─ BEASTInterfaceTest ✔ - [java] │ │ ├─ testInputType() ✔ - [java] │ │ └─ testBEASTi() ✔ [java] │ ├─ LoggerTest ✔ [java] │ │ ├─ testFileLog() ✔ [java] │ │ ├─ testScreenLog() ✔ @@ -15443,15 +15480,20 @@ [java] │ │ ├─ testJSON() ✔ [java] │ │ ├─ testInnerClass() ✔ [java] │ │ └─ testPrimitiveInput() ✔ + [java] │ ├─ BEASTInterfaceTest ✔ + [java] │ │ ├─ testInputType() ✔ + [java] │ │ └─ testBEASTi() ✔ + [java] │ ├─ BooleanParameterListTest ✔ + [java] │ │ └─ test1() ✔ [java] │ ├─ InputTest ✔ [java] │ │ ├─ testOptionalInput() ✔ [java] │ │ ├─ testScientificNotationDecimalFailure() ✔ [java] │ │ ├─ testScienticNotation() ✔ [java] │ │ └─ testScientificNotationIntTooLarge() ✔ - [java] │ ├─ BooleanParameterListTest ✔ - [java] │ │ └─ test1() ✔ [java] │ ├─ IntegerParameterListTest ✔ [java] │ │ └─ test1() ✔ + [java] │ ├─ SumTest ✔ + [java] │ │ └─ testSum() ✔ [java] │ ├─ OperatorScheduleTest ✔ [java] │ │ ├─ testOperatorScheduleMultiNestedByPercentageAndRelativeWeight() ✔ [java] │ │ ├─ testOperatorScheduleNestedByPercentage() ✔ @@ -15461,20 +15503,22 @@ [java] │ │ ├─ testOperatorScheduleNestedByRelativeWeight() ✔ [java] │ │ ├─ testOperatorSchedulePlain() ✔ [java] │ │ └─ testOperatorScheduleNestedByRelativeWeight2() ✔ - [java] │ ├─ SumTest ✔ - [java] │ │ └─ testSum() ✔ [java] │ ├─ DataTypeDeEncodeTest ✔ [java] │ │ └─ testDataTypeDeEncode() ✔ + [java] │ ├─ BactrianIntervalOperatorTest ✔ + [java] │ │ ├─ testLogNormalDistribution() ✔ + [java] │ │ ├─ testNormalDistribution() ✔ + [java] │ │ ├─ testUniformDistributionZeroUpperBound() ✔ + [java] │ │ ├─ testUniformDistribution() ✔ + [java] │ │ └─ testUniformDistributionZeroLowerBound() ✔ [java] │ ├─ UncertainAlignmentTest ✔ [java] │ │ └─ testUncertainAlignment() ✔ - [java] │ ├─ BactrianIntervalOperatorTest ✔ - [java] │ │ ├─ testLogNormalDistribution() 35038 ms ✔ - [java] │ │ ├─ testNormalDistribution() 29786 ms ✔ - [java] │ │ ├─ testUniformDistributionZeroUpperBound() 35574 ms ✔ - [java] │ │ ├─ testUniformDistribution() 39726 ms ✔ - [java] │ │ └─ testUniformDistributionZeroLowerBound() 37643 ms ✔ [java] │ ├─ GeneralSubstitutionModelTest ✔ [java] │ │ └─ getTransitionProbabilities() ✔ + [java] │ ├─ DeltaExchangeOperatorTest ✔ + [java] │ │ ├─ testKeepsSum() ✔ + [java] │ │ ├─ testCanOperate() ✔ + [java] │ │ └─ testKeepsWeightedSum() ✔ [java] │ ├─ BeagleTreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15511,10 +15555,6 @@ [java] │ │ ├─ testAminoAcidLikelihoodcpRev() ✔ [java] │ │ ├─ testAminoAcidLikelihoodBlosum62() ✔ [java] │ │ └─ testAminoAcidLikelihoodGIDayhoff() ✔ - [java] │ ├─ DeltaExchangeOperatorTest ✔ - [java] │ │ ├─ testKeepsSum() ✔ - [java] │ │ ├─ testCanOperate() ✔ - [java] │ │ └─ testKeepsWeightedSum() ✔ [java] │ ├─ BactrianScaleOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testTwoDimensionalDistribution() ✔ @@ -15523,9 +15563,9 @@ [java] │ │ ├─ testScaleAllIndependentlylDistribution() ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() 28848 ms ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() 22408 ms ✔ - [java] │ │ └─ testNarrowExchange6Taxa() 22795 ms ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() ✔ + [java] │ │ └─ testNarrowExchange6Taxa() ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ @@ -15545,7 +15585,7 @@ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistribution() ✔ [java] │ │ ├─ testMultiDimensionalMirrorfKernelDistributionScaler() ✔ [java] │ │ ├─ testMirrorfKernelDistribution() ✔ - [java] │ │ └─ testBactrianKernelDistribution() 10900 ms ✔ + [java] │ │ └─ testBactrianKernelDistribution() ✔ [java] │ ├─ FilteredAlignmentTest ✔ [java] │ │ ├─ testWeightedSites() ✔ [java] │ │ ├─ testFilteredFileredAlignment() ✔ @@ -15561,17 +15601,17 @@ [java] │ ├─ TreeTest ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x6() 11598 ms ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() 34581 ms ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() 23917 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x6() ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() 10442 ms ✔ - [java] │ │ └─ testLogNormalDistribution() 11855 ms ✔ + [java] │ │ ├─ testNormalDistribution() ✔ + [java] │ │ └─ testLogNormalDistribution() ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 39697 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 12189 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15614,10 +15654,10 @@ [java] │ │ └─ testSkyline() ✔ [java] │ ├─ CompoundParameterHelperTest ✔ [java] │ │ └─ testCompoundParameterHelper() ✔ + [java] │ ├─ RandomTreeTest ✔ + [java] │ │ └─ testCoalescentTimes() 10445 ms ✔ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ - [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 31547 ms ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ [java] │ │ └─ testJC69Likelihood() ✔ [java] │ ├─ LaplaceDistributionTest ✔ @@ -15674,7 +15714,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 482922 ms + [java] Test run finished after 90975 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15688,14 +15728,10 @@ [java] [ 207 tests successful ] [java] [ 0 tests failed ] [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. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null614654240 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1607252866 [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: 2644ms -[junitreport] Deleting: /tmp/null614654240 +[junitreport] Transform time: 568ms +[junitreport] Deleting: /tmp/null1607252866 junit-integration: [java] @@ -15735,7 +15771,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1979 ms + [java] Test run finished after 644 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15753,10 +15789,10 @@ [java] WARNING: Delegated to the 'execute' command. [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1120109218 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null1653231635 [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: 849ms -[junitreport] Deleting: /tmp/null1120109218 +[junitreport] Transform time: 131ms +[junitreport] Deleting: /tmp/null1653231635 junit-xmlparsertest: [java] @@ -15769,7 +15805,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1278 ms + [java] Test run finished after 284 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15787,15 +15823,15 @@ [java] WARNING: Delegated to the 'execute' command. [java] This behaviour has been deprecated and will be removed in a future release. [java] Please use the 'execute' command directly. -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null1842252249 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null1426229978 [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: 389ms -[junitreport] Deleting: /tmp/null1842252249 +[junitreport] Transform time: 65ms +[junitreport] Deleting: /tmp/null1426229978 junit: BUILD SUCCESSFUL -Total time: 8 minutes 29 seconds +Total time: 1 minute 35 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15824,8 +15860,8 @@ 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_amd64.buildinfo dpkg-genchanges --build=binary -O../beast2-mcmc_2.7.6+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -15833,12 +15869,14 @@ 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/2428908/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2428908/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/875119 and its subdirectories -I: Current time: Mon May 6 17:45:09 -12 2024 -I: pbuilder-time-stamp: 1715060709 +I: removing directory /srv/workspace/pbuilder/2428908 and its subdirectories +I: Current time: Tue Jun 10 02:11:39 +14 2025 +I: pbuilder-time-stamp: 1749471099