Diff of the two buildlogs: -- --- b1/build.log 2024-05-02 09:27:32.906121062 +0000 +++ b2/build.log 2024-05-02 09:36:39.666814385 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed May 1 21:07:44 -12 2024 -I: pbuilder-time-stamp: 1714640864 +I: Current time: Thu May 2 23:27:41 +14 2024 +I: pbuilder-time-stamp: 1714642061 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/15150/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/25718/tmp/hooks/D01_modify_environment starting +debug: Running on virt64z. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 2 09:27 /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/25718/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/25718/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='f33bc83c3a1d4e0e824a2c09be9e7fcc' - 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='15150' - PS1='# ' - PS2='> ' + INVOCATION_ID=63a1f3eba0214b4dbcaa5da8d392ec34 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=25718 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.CFiNYIhy/pbuilderrc_LqDX --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CFiNYIhy/b1 --logfile b1/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' - SUDO_GID='112' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CFiNYIhy/pbuilderrc_RLHs --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CFiNYIhy/b2 --logfile b2/build.log beast2-mcmc_2.7.6+dfsg-1.dsc' + SUDO_GID=110 + SUDO_UID=103 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32b 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 1 07:44 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/15150/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 1 07:43 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/25718/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -466,7 +498,7 @@ Get: 317 http://deb.debian.org/debian unstable/main armhf libjam-java all 0.1.git20180106.740247a+dfsg-1 [164 kB] Get: 318 http://deb.debian.org/debian unstable/main armhf libopenjfx-jni armhf 11.0.11+1-3.2 [18.0 MB] Get: 319 http://deb.debian.org/debian unstable/main armhf libopenjfx-java all 11.0.11+1-3.2 [8903 kB] -Fetched 323 MB in 1min 1s (5283 kB/s) +Fetched 323 MB in 17s (19.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19440 files and directories currently installed.) @@ -1522,8 +1554,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu May 2 09:15:13 UTC 2024. -Universal Time is now: Thu May 2 09:15:13 UTC 2024. +Local time is now: Thu May 2 09:29:19 UTC 2024. +Universal Time is now: Thu May 2 09:29:19 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -1980,7 +2012,11 @@ 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/25718/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/25718/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 @@ -1996,7 +2032,7 @@ clean: BUILD SUCCESSFUL -Total time: 1 second +Total time: 0 seconds jh_clean debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' @@ -2099,7 +2135,7 @@ [jar] Building jar: /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/dist/BEAST.app.jar BUILD SUCCESSFUL -Total time: 1 minute 44 seconds +Total time: 48 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' @@ -2122,14 +2158,7 @@ [java] 768 sites [java] 69 patterns [java] - [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 taxaOK + [java] OK [java] test getCitation [java] test initByName [java] test listInputs @@ -2137,7 +2166,14 @@ [java] test getInputValue [java] test getOutputs [java] Validation error when initializing object test.beast.core.BEASTInterfaceTest$BEASTi (id null): - [java] + [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] @@ -2147,13 +2183,41 @@ [java] {spec: "test.beast.core.PrimitiveBeastObject", e: "none", i: "0", a: [3.0, 4.0] } [java] ] [java] } - [java] Failed to set the string value to '1e-1' for beastobject id=null [java] Writing file beast.log [java] Sample null.1 null.2 [java] 1 0.3 0.7 -- + [java] Failed to set the string value to '1e-1' for beastobject id=null [java] Failed to set the string value to '21474836470' for beastobject id=null [java] WARNING: Operator scaleOperator.Species is contained in multiple operator schedules. [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] @@ -2178,7 +2242,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.361 seconds + [java] Total calculation time: 2.867 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 @@ -2210,14 +2274,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.417 seconds + [java] Total calculation time: 2.881 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.4999085326599657 variance: 0.009984682019634223 ESS: 199303.5697419057 [java] ------------------------------------------------- [java] - [java] trace log written to /tmp/bactrian.log [java] End likelihood: 1.3580153849800576 + [java] trace log written to /tmp/bactrian.log [java] =============================================================================== [java] Citations for this model: [java] @@ -2242,7 +2306,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.427 seconds + [java] Total calculation time: 2.773 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: -0.9999141170712793 variance: 0.33333524355317856 ESS: 198672.26933150293 @@ -2274,7 +2338,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.902 seconds + [java] Total calculation time: 2.564 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 2.000085882932697 variance: 0.3333352435532261 ESS: 198672.26933142878 @@ -2306,14 +2370,14 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.959 seconds + [java] Total calculation time: 2.59 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0000858834576856 variance: 0.3333352435537048 ESS: 198672.26933242727 [java] ------------------------------------------------- [java] - [java] End likelihood: -0.6931471805599453 [java] trace log written to /tmp/bactrian.log + [java] End likelihood: -0.6931471805599453 [java] Validation error when initializing object beast.base.inference.operator.DeltaExchangeOperator (id null): [java] java.lang.IllegalArgumentException: Input 'weight' must be specified. [java] at beast.base.core.Input.validate(Unknown Source) @@ -2332,11 +2396,40 @@ [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] Starting frequencies: [0.3333333, 0.3333333, 0.3333333] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) + [java] freqs = + [java] [0.3333333, 0.3333333, 0.3333333] + [java] + [java] relative rates : + [java] [0.1, 0.0, 0.1, 0.2, 0.0, 0.2] + [java] + [java] + [java] renormalised rate matrix : + [java] [1.0, -2.4928748491937626E-16, -3.386149245429483E-17] + [java] [2.69374457498681E-22, 1.0, -1.9925481744283377E-16] + [java] [3.749348770303284E-12, 6.1384477687519146E-18, 1.0] + [java] + [java] transition prob : + [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] + [java] row 0 prob sum = 0.9999999999999996 + [java] row 1 prob sum = 0.9999999999999998 + [java] row 2 prob sum = 0.9999999999999999 + [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) @@ -2422,63 +2515,6 @@ [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == [java] ============================================================================================================== [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] 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] - [java] - [java] relative rates : - [java] [0.1, 0.0, 0.1, 0.2, 0.0, 0.2] - [java] - [java] - [java] renormalised rate matrix : - [java] [1.0, -2.4928748491937626E-16, -3.386149245429483E-17] - [java] [2.69374457498681E-22, 1.0, -1.9925481744283377E-16] - [java] [3.749348770303284E-12, 6.1384477687519146E-18, 1.0] - [java] - [java] transition prob : - [java] [0.6674871505723157, 0.22927797953210746, 0.10323486989557647, 0.2292779795321076, 0.415400931299253, 0.35532108916863914, 0.10323486989557647, 0.3553210891686388, 0.5414440409357847] - [java] row 0 prob sum = 0.9999999999999996 - [java] row 1 prob sum = 0.9999999999999998 - [java] row 2 prob sum = 0.9999999999999999 - [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. @@ -2496,19 +2532,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 69 unique site patterns. [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] human: 772 4 [java] chimp: 772 4 [java] bonobo: 772 4 @@ -2550,6 +2573,30 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX + [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 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [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. == @@ -2573,17 +2620,15 @@ [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 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX + [java] 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] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -2600,20 +2645,6 @@ [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] 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] German_ST: 5051 2 [java] Dutch_List: 5051 2 [java] English_ST: 5051 2 @@ -2641,14 +2672,7 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 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] 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. == @@ -2656,7 +2680,11 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. + [java] With 50 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Using ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 50 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -2676,7 +2704,6 @@ [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 [java] Pterocnemia_pennata: 85 20 @@ -2699,28 +2726,6 @@ [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] - [java] ============================================================================================================== - [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] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 [java] Pterocnemia_pennata: 85 20 @@ -2758,6 +2763,19 @@ [java] 69 patterns [java] [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] 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] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -2765,11 +2783,7 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Using ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. + [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic [java] ============================================================================================================== [java] ============================================================================================================== @@ -2787,12 +2801,12 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] 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. == @@ -2800,25 +2814,21 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none + [java] 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] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] 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] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX [java] seq1: 3 4 @@ -2870,67 +2880,6 @@ [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE [java] -12.421114302827698 [java] Without tip likelihoods: - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 3 unique site patterns. - [java] Using rescaling scheme : none - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none - [java] Ignoring ambiguities in tree likelihood. - [java] Using character uncertainty in tree likelihood. - [java] With 6 unique site patterns. - [java] Using rescaling scheme : none - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 64 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE PRECISION_DOUBLE [java] -12.421114302827698 @@ -2995,32 +2944,6 @@ [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] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 69 unique site patterns. - [java] Using rescaling scheme : dynamic [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL @@ -3065,6 +2988,119 @@ [java] ============================================================================================================== [java] Ignoring ambiguities in tree likelihood. [java] Ignoring character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 3 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none + [java] Ignoring ambiguities in tree likelihood. + [java] Using character uncertainty in tree likelihood. + [java] With 6 unique site patterns. + [java] Using rescaling scheme : none + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 64 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 64 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] Ignoring ambiguities in tree likelihood. + [java] Ignoring character uncertainty in tree likelihood. + [java] With 32 unique site patterns. + [java] Using rescaling scheme : dynamic + [java] ============================================================================================================== + [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 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 69 unique site patterns. [java] Using rescaling scheme : dynamic [java] Using ambiguities in tree likelihood. @@ -3084,6 +3120,15 @@ [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] human: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -3120,15 +3165,26 @@ [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 32 unique site patterns. - [java] Using rescaling scheme : dynamic + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: COMPUTATION_ASYNCH + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: COMPUTATION_ASYNCH + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] ============================================================================================================== [java] ============================================================================================================== [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == @@ -3155,26 +3211,11 @@ [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: COMPUTATION_ASYNCH - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: COMPUTATION_ASYNCH - [java] human: 768 4 - [java] chimp: 768 4 - [java] bonobo: 768 4 - [java] gorilla: 768 4 - [java] orangutan: 768 4 - [java] siamang: 768 4 - [java] Alignment(null) - [java] 6 taxa - [java] 768 sites - [java] 69 patterns - [java] - [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [java] ============================================================================================================== + [java] ============================================================================================================== [java] German_ST: 5051 4 [java] Dutch_List: 5051 4 [java] English_ST: 5051 4 @@ -3190,28 +3231,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 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] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_DOUBLE EIGEN_REAL EIGEN_COMPLEX [java] Starting frequencies: [0.07207207207207206, 0.006006006006006005, 0.019019019019019014, 0.02402402402402402, 0.061061061061061045, 0.05605605605605604, 0.02802802802802802, 0.08808808808808806, 0.023023023023023018, 0.16816816816816815, 0.05405405405405404, 0.039039039039039033, 0.05405405405405404, 0.02502502502502502, 0.019019019019019014, 0.07207207207207206, 0.08608608608608606, 0.04304304304304303, 0.029029029029029024, 0.033033033033033024] @@ -3236,18 +3255,23 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [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] 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. == @@ -3279,6 +3303,18 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic + [java] human: 768 4 + [java] chimp: 768 4 + [java] bonobo: 768 4 + [java] gorilla: 768 4 + [java] orangutan: 768 4 + [java] siamang: 768 4 + [java] Alignment(null) + [java] 6 taxa + [java] 768 sites + [java] 69 patterns + [java] + [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: PRECISION_SINGLE COMPUTATION_SYNCH SCALING_MANUAL [java] Using BEAGLE version: 3.1.2 resource 0: CPU @@ -3316,6 +3352,35 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX + [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] + [java] Struthio_camelus: 85 20 + [java] Rhea_americana: 85 20 + [java] Pterocnemia_pennata: 85 20 + [java] Alignment(null) + [java] 3 taxa + [java] 85 sites + [java] 32 patterns + [java] + [java] Using BEAGLE version: 3.1.2 resource 0: CPU + [java] with instance flags: EIGEN_COMPLEX + [java] ============================================================================================================== + [java] ============================================================================================================== + [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == + [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. == @@ -3343,17 +3408,6 @@ [java] Ignoring character uncertainty in tree likelihood. [java] With 32 unique site patterns. [java] Using rescaling scheme : dynamic - [java] Starting frequencies: [0.076, 0.009, 0.037, 0.049, 0.051, 0.084, 0.025, 0.081, 0.05, 0.101, 0.022, 0.041, 0.043, 0.038, 0.062, 0.062, 0.054, 0.066, 0.018, 0.031] - [java] Struthio_camelus: 85 20 - [java] Rhea_americana: 85 20 - [java] Pterocnemia_pennata: 85 20 - [java] Alignment(null) - [java] 3 taxa - [java] 85 sites - [java] 32 patterns - [java] - [java] Using BEAGLE version: 3.1.2 resource 0: CPU - [java] with instance flags: EIGEN_COMPLEX [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -3376,24 +3430,6 @@ [java] [java] Using BEAGLE version: 3.1.2 resource 0: CPU [java] with instance flags: EIGEN_COMPLEX - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] == Make sure to have BEAGLE installed and set the -Djava.library.path=/path/to/beagle option for this test. == - [java] ============================================================================================================== - [java] ============================================================================================================== - [java] Ignoring ambiguities in tree likelihood. - [java] Ignoring character uncertainty in tree likelihood. - [java] With 32 unique site patterns. - [java] Using rescaling scheme : dynamic [java] =============================================================================== [java] Citations for this model: [java] @@ -3418,7 +3454,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.565 seconds + [java] Total calculation time: 1.841 seconds [java] End likelihood: -2.101581781210349 [java] =============================================================================== [java] Citations for this model: @@ -3433,7 +3469,6 @@ [java] [java] =============================================================================== [java] Start likelihood: -7.148765227934941 - [java] End likelihood: 0.008929267909451477 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 2.31053 307447 692554 1.00000 0.30745 @@ -3445,7 +3480,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 3.942 seconds + [java] Total calculation time: 1.424 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3459,6 +3494,8 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 + [java] End likelihood: 0.008929267909451477 + [java] End likelihood: -0.5552616722623194 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.33125 153295 347047 0.50000 0.30638 @@ -3471,8 +3508,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 4.701 seconds - [java] End likelihood: -0.5552616722623194 + [java] Total calculation time: 2.184 seconds [java] =============================================================================== [java] Citations for this model: [java] @@ -3486,6 +3522,7 @@ [java] [java] =============================================================================== [java] Start likelihood: -21.446295683804824 + [java] End likelihood: -2.422052674651341 [java] [java] Operator Tuning #accept #reject Pr(m) Pr(acc|m) [java] kernel.BactrianScaleOperator(unknown) 1.23542 303560 696441 1.00000 0.30356 @@ -3497,8 +3534,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 7.242 seconds - [java] End likelihood: -2.422052674651341 + [java] Total calculation time: 2.702 seconds [java] A: 1 4 [java] B: 1 4 [java] C: 1 4 @@ -3546,6 +3582,8 @@ [java] =============================================================================== [java] Start likelihood: 0.6286086594223761 [java] End likelihood: 3.119201359019653 + [java] Testing mirror distribution + [java] Testing mirror distribution for scaling [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 @@ -3557,9 +3595,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 2.163 seconds - [java] Testing mirror distribution - [java] Testing mirror distribution for scaling + [java] Total calculation time: 1.464 seconds [java] kick in [java] kick in [java] kick in @@ -3586,8 +3622,6 @@ [java] Testing bactrian_triangle s= 0.999423750532334 [java] Testing bactrian_triangle s= 0.9998030418762279 [java] Testing bactrian_box s= 0.9993617332307378 - [java] Testing bactrian_box s= 0.9993638943013682 - [java] Number of weights (4) does not match sequence length (16) [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) @@ -3599,7 +3633,25 @@ [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa - [java] 16 sites + [java] Testing bactrian_box s= 0.9993638943013682 + [java] Number of weights (4) does not match sequence length (16) + [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4] + [java] 0human AAAACCCCGGGGTTTT + [java] 1chimp ACGTACGTACGTACGT + [java] 16 sites[11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] AAAACCCCTTTTGGGG + [java] ACTGACGTACGTACGT + [java] [101000, 10000, 1, 110] + [java] GGGAAA + [java] AGGACA + [java] java.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) + [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) + [java] at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) + [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) + [java] [java] 16 patterns [java] [java] 0human: 16 4 @@ -3609,7 +3661,29 @@ [java] 16 sites with weight 12514 [java] 16 patterns [java] - [java] 0human: 16 4 + [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)0human: 16 4 + [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] [java] 1chimp: 16 4 [java] Alignment(null) [java] 2 taxa @@ -3685,35 +3759,24 @@ [java] 2 taxa [java] 8 sites + 11241 constant sites [java] 10 patterns - [java] [11232, 2, 3, 4, 1123, 2, 3, 4, 112, 2, 3, 4, 11, 2, 3, 4]Stripping invariant sitesFilter -8 - [java] 0human AAAACCCCGGGGTTTT - [java] 1chimp ACGTACGTACGTACGT - [java] + [java] Stripping invariant sitesFilter -8 [java] 2 taxa [java] 8 sites + 11241 constant sites - [java] 10 patterns[11232, 2, 4, 3, 1123, 2, 3, 4, 11, 2, 3, 4, 112, 2, 3, 4] + [java] 10 patterns [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) - [java] AAAACCCCTTTTGGGG - [java] ACTGACGTACGTACGT - [java] [101000, 10000, 1, 110] [java] 2 taxa - [java] - [java] GGGAAA - [java] AGGACA 16 sites - [java] + [java] 16 sites [java] 12 patterns [java] [java] Filter 3:6:1 [java] 2 taxa - [java] 4 sitesjava.lang.RuntimeException: Cannot handle site weights in FilteredAlignment. Remove "weights" from data input. + [java] 4 sites [java] 4 patterns [java] human AACC - [java] [java] 1chimp GTAC - [java] Filter 11:14:1 at beast.base.evolution.alignment.FilteredAlignment.calcPatterns(Unknown Source) - [java] at beast.base.evolution.alignment.FilteredAlignment.initAndValidate(Unknown Source) + [java] Filter 11:14:1 [java] 2 taxa [java] 4 sites [java] 4 patterns @@ -3753,138 +3816,12 @@ [java] 0human: 16 4 [java] 1chimp: 16 4 [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] Filter 1-9 - [java] 2 taxa - [java] 9 sites - [java] 9 patterns - [java] Filter 2-9 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 10- - [java] 2 taxa - [java] 7 sites - [java] 7 patterns - [java] Filter -10 - [java] 2 taxa - [java] 10 sites - [java] 10 patterns - [java] Filter - - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] Filter 2-5,7-10 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] 0human: 16 4 - [java] 1chimp: 16 4 - [java] Alignment(null) - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] - [java] Filter 1:16:2 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 2:16:2 - [java] 2 taxa - [java] 8 sites - [java] 8 patterns - [java] Filter 1:10:2 - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] Filter 1::3 - [java] 2 taxa - [java] 6 sites - [java] 6 patterns - [java] Filter 2::3 - [java] 2 taxa - [java] 5 sites - [java] 5 patterns - [java] Filter :: - [java] 2 taxa - [java] 16 sites - [java] 16 patterns - [java] Filter 2:5: - [java] 2 taxa - [java] 4 sites - [java] 4 patterns - [java] Filter :5: - [java] at beast.base.core.BEASTInterface.initByName(Unknown Source) - [java] - [java] 2 taxa - [java] 5 sites at test.beast.evolution.alignment.FilteredAlignmentTest.testWeightedSites(Unknown Source) - [java] - [java] at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) - [java] 5 patterns at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) - [java] Filter 1::3,2::3 - [java] 2 taxa - [java] at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) - [java] - [java] 11 sites - [java] 11 patterns at java.base/java.lang.reflect.Method.invoke(Method.java:568) - [java] Filter 3::3 - [java] at org.junit.platform.commons.util.ReflectionUtils.invokeMethod(ReflectionUtils.java:728) - [java] - [java] 2 taxa - [java] at org.junit.jupiter.engine.execution.MethodInvocation.proceed(MethodInvocation.java:60)5 sites - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain$ValidatingInvocation.proceed(InvocationInterceptorChain.java:131) - [java] - [java] 5 patterns - [java] t0: 1 4 at org.junit.jupiter.engine.extension.TimeoutExtension.intercept(TimeoutExtension.java:156) - [java] t1: 1 4 - [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] - [java] Alignment(null) - [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$0(InterceptingExecutableInvoker.java:93) - [java] 2 taxa at org.junit.jupiter.engine.execution.InvocationInterceptorChain$InterceptedInvocation.proceed(InvocationInterceptorChain.java:106) - [java] 1 site - [java] - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.proceed(InvocationInterceptorChain.java:64) - [java] - [java] t0 = 0 (10.0) - [java] t1 = 10 (0.0) at org.junit.jupiter.engine.execution.InvocationInterceptorChain.chainAndInvoke(InvocationInterceptorChain.java:45) - [java] t0: 1 4 - [java] at org.junit.jupiter.engine.execution.InvocationInterceptorChain.invoke(InvocationInterceptorChain.java:37) - [java] - [java] t1: 1 4 at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:92) - [java] Alignment(null) - [java] at org.junit.jupiter.engine.execution.InterceptingExecutableInvoker.invoke(InterceptingExecutableInvoker.java:86) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.lambda$invokeTestMethod$7(TestMethodTestDescriptor.java:218) [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] - [java] 2 taxa - [java] 1 site at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.invokeTestMethod(TestMethodTestDescriptor.java:214) - [java] - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:139) - [java] at org.junit.jupiter.engine.descriptor.TestMethodTestDescriptor.execute(TestMethodTestDescriptor.java:69) - [java] - [java] t0 = null (0.0) - [java] t1 = 10 (0.0) at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$6(NodeTestTask.java:151) - [java] - [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] t0: 1 4 at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) - [java] t1: 1 4 - [java] Alignment(null) + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$8(NodeTestTask.java:141) [java] at org.junit.platform.engine.support.hierarchical.Node.around(Node.java:137) - [java] - [java] 2 taxa - [java] 1 site at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) - [java] + [java] at org.junit.platform.engine.support.hierarchical.NodeTestTask.lambda$executeRecursively$9(NodeTestTask.java:139) [java] at org.junit.platform.engine.support.hierarchical.ThrowableCollector.execute(ThrowableCollector.java:73) - [java] - [java] t0 = 0 (0.0) - [java] t1 = 10 (10.0) at org.junit.platform.engine.support.hierarchical.NodeTestTask.executeRecursively(NodeTestTask.java:138) - [java] + [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) @@ -4008,6 +3945,105 @@ [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] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] Filter 1-9 + [java] 2 taxa + [java] 9 sites + [java] 9 patterns + [java] Filter 2-9 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 10- + [java] 2 taxa + [java] 7 sites + [java] 7 patterns + [java] Filter -10 + [java] 2 taxa + [java] 10 sites + [java] 10 patterns + [java] Filter - + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] Filter 2-5,7-10 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] 0human: 16 4 + [java] 1chimp: 16 4 + [java] Alignment(null) + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] + [java] Filter 1:16:2 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 2:16:2 + [java] 2 taxa + [java] 8 sites + [java] 8 patterns + [java] Filter 1:10:2 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter 1::3 + [java] 2 taxa + [java] 6 sites + [java] 6 patterns + [java] Filter 2::3 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter :: + [java] 2 taxa + [java] 16 sites + [java] 16 patterns + [java] Filter 2:5: + [java] 2 taxa + [java] 4 sites + [java] 4 patterns + [java] Filter :5: + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] Filter 1::3,2::3 + [java] 2 taxa + [java] 11 sites + [java] 11 patterns + [java] Filter 3::3 + [java] 2 taxa + [java] 5 sites + [java] 5 patterns + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = 0 (10.0) + [java] t1 = 10 (0.0) + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = null (0.0) + [java] t1 = 10 (0.0) + [java] t0: 1 4 + [java] t1: 1 4 + [java] Alignment(null) + [java] 2 taxa + [java] 1 site + [java] + [java] t0 = 0 (0.0) + [java] t1 = 10 (10.0) [java] 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) @@ -4103,7 +4139,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 6.932 seconds + [java] Total calculation time: 4.476 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.9998844142873523 variance: 0.9962228119352534 ESS: 194315.96975231904 @@ -4135,7 +4171,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 7.077 seconds + [java] Total calculation time: 4.786 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 1.0017946084516174 variance: 1.7216547315129034 ESS: 25717.88066360503 @@ -4143,14 +4179,6 @@ [java] [java] trace log written to /tmp/bactrian.log [java] End likelihood: -0.8084620917497215 - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] - [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. - [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] - [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] @@ -4170,13 +4198,31 @@ [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] Expected: [0.05870763770495499, 0.4129812075958677, 0.06575499966675094, 0.46255615503242636] + [java] Calculat: [0.058707637705059205, 0.41298120759660106, 0.06575499966686761, 0.46255615503324765, 0.05870763770505924, 0.4129812075966013, 0.06575499966686764, 0.4625561550332479, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482, 0.05870763770505928, 0.41298120759660156, 0.0657549996668677, 0.4625561550332482] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package.Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. + [java] If you encounter infinities, or chains getting stuck, consider using a more robust eigen system, by setting the eigenSystem input, e.g. eigenSystem="beast.evolution.substitutionmodel.RobustEigenSystem" available from the beast-classic package. [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25] + [java] + [java] Starting frequencies: [0.25, 0.25, 0.25, 0.25]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] =============================================================================== [java] Citations for this model: [java] - [java] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, + [java] + [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] Bouckaert, Remco, Timothy G. Vaughan, Joëlle Barido-Sottani, Sebastián Duchêne, Mathieu Fourment, 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] + [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] Alexandra Gavryushkina, Joseph Heled, Graham Jones, Denise Kühnert, Nicola De Maio, Michael Matschiner, + [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] Fábio K. Mendes, Nicola F. Müller, Huw A. Ogilvie, Louis du Plessis, Alex Popinga, Andrew Rambaut, + [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] David Rasmussen, Igor Siveroni, Marc A. Suchard, Chieh-Hsi Wu, Dong Xie, Chi Zhang, Tanja Stadler, [java] Alexei J. Drummond [java] BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. @@ -4184,16 +4230,6 @@ [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] 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 @@ -4207,7 +4243,7 @@ [java] Pr(acc|m): The acceptance probability (#accept as a fraction of the total proposals for this operator). [java] [java] - [java] Total calculation time: 23.495 seconds + [java] Total calculation time: 16.604 seconds [java] [java] ----- Tree trace analysis ----------------------- [java] Mean: 0.999687438963848 variance: 1.6815511765072393 ESS: 106131.3927120149 @@ -4215,6 +4251,10 @@ [java] [java] End likelihood: -0.20113760213898557 [java] trace log written to /tmp/bactrian.log + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. + [java] WARNING: found multiple entries for a site that occurs multiple times and is ascertained for. This may indicate some sites should be removed. Regardless, these sites will be ignored in the likelihood calculation. [java] Starting frequencies: [0.074, 0.025, 0.054, 0.054, 0.047, 0.074, 0.026, 0.068, 0.058, 0.099, 0.025, 0.045, 0.039, 0.034, 0.052, 0.057, 0.051, 0.073, 0.013, 0.032] [java] Struthio_camelus: 85 20 [java] Rhea_americana: 85 20 @@ -4254,6 +4294,7 @@ [java] Starting frequencies: [0.3390942900867236, 0.24655436447178358, 0.1531393568179342, 0.26121198862355866] [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] + [java] 9.094947017729282E-13 [java] TreeLikelihood(null) uses BeerLikelihoodCore4 [java] Alignment(null): [taxa, patterns, sites] = [6, 69, 768] [java] Starting frequencies: [0.077, 0.02, 0.052, 0.062, 0.04, 0.074, 0.023, 0.052, 0.059, 0.091, 0.024, 0.043, 0.051, 0.041, 0.051, 0.069, 0.059, 0.066, 0.014, 0.032] @@ -4278,10 +4319,6 @@ [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: 768 4 [java] chimp: 768 4 [java] bonobo: 768 4 @@ -4347,7 +4384,6 @@ [java] [java] TreeLikelihood(null) uses BeerLikelihoodCore [java] Alignment(null): [taxa, patterns, sites] = [3, 32, 85] - [java] 9.094947017729282E-13 [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 @@ -15048,7 +15084,6 @@ [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] adfgad [java] java.lang.reflect.InvocationTargetException [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) [java] at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77) @@ -15354,6 +15389,13 @@ [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] 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] 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) @@ -15396,12 +15438,6 @@ [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] 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. @@ -15457,16 +15493,16 @@ [java] │ │ └─ testOperatorScheduleNestedByRelativeWeight2() ✔ [java] │ ├─ SumTest ✔ [java] │ │ └─ testSum() ✔ - [java] │ ├─ DataTypeDeEncodeTest ✔ - [java] │ │ └─ testDataTypeDeEncode() ✔ - [java] │ ├─ BactrianIntervalOperatorTest ✔ - [java] │ │ ├─ testLogNormalDistribution() 27210 ms ✔ - [java] │ │ ├─ testNormalDistribution() 23896 ms ✔ - [java] │ │ ├─ testUniformDistributionZeroUpperBound() 21895 ms ✔ - [java] │ │ ├─ testUniformDistribution() 20880 ms ✔ - [java] │ │ └─ testUniformDistributionZeroLowerBound() 20908 ms ✔ [java] │ ├─ UncertainAlignmentTest ✔ [java] │ │ └─ testUncertainAlignment() ✔ + [java] │ ├─ BactrianIntervalOperatorTest ✔ + [java] │ │ ├─ testLogNormalDistribution() 11710 ms ✔ + [java] │ │ ├─ testNormalDistribution() 11353 ms ✔ + [java] │ │ ├─ testUniformDistributionZeroUpperBound() 10655 ms ✔ + [java] │ │ ├─ testUniformDistribution() 11296 ms ✔ + [java] │ │ └─ testUniformDistributionZeroLowerBound() 11166 ms ✔ + [java] │ ├─ DataTypeDeEncodeTest ✔ + [java] │ │ └─ testDataTypeDeEncode() ✔ [java] │ ├─ GeneralSubstitutionModelTest ✔ [java] │ │ └─ getTransitionProbabilities() ✔ [java] │ ├─ DeltaExchangeOperatorTest ✔ @@ -15517,19 +15553,19 @@ [java] │ │ ├─ testScaleAllIndependentlylDistribution() ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ ExchangeOperatorTest ✔ - [java] │ │ ├─ testNarrowExchange4Taxa() 19355 ms ✔ - [java] │ │ ├─ testNarrowExchange5Taxa() 17178 ms ✔ - [java] │ │ └─ testNarrowExchange6Taxa() 17509 ms ✔ + [java] │ │ ├─ testNarrowExchange4Taxa() 12092 ms ✔ + [java] │ │ ├─ testNarrowExchange5Taxa() 10500 ms ✔ + [java] │ │ └─ testNarrowExchange6Taxa() 10858 ms ✔ [java] │ ├─ BactrianDeltaExchangeOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ [java] │ │ ├─ testLogNormalDistribution() ✔ [java] │ │ ├─ testKeepsSum() ✔ [java] │ │ ├─ testCanOperate() ✔ [java] │ │ └─ testKeepsWeightedSum() ✔ - [java] │ ├─ YuleModelTest ✔ - [java] │ │ └─ testYule() ✔ [java] │ ├─ ScaleOperatorTest ✔ [java] │ │ └─ testTreeScaling() ✔ + [java] │ ├─ YuleModelTest ✔ + [java] │ │ └─ testYule() ✔ [java] │ ├─ NodeTest ✔ [java] │ │ ├─ testToNewick() ✔ [java] │ │ ├─ testRootToString() ✔ @@ -15555,17 +15591,17 @@ [java] │ ├─ TreeTest ✔ [java] │ │ └─ testTreeScaling() ✔ [java] │ ├─ IntRandomWalkOperatorTest ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x6() 10949 ms ✔ - [java] │ │ ├─ testIntRandomWalkDistribution3x10() 30575 ms ✔ - [java] │ │ └─ testIntRandomWalkDistribution6x10() 58244 ms ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x6() ✔ + [java] │ │ ├─ testIntRandomWalkDistribution3x10() 22735 ms ✔ + [java] │ │ └─ testIntRandomWalkDistribution6x10() 40030 ms ✔ [java] │ ├─ BactrianRandomWalkOperatorTest ✔ - [java] │ │ ├─ testNormalDistribution() 23560 ms ✔ - [java] │ │ └─ testLogNormalDistribution() 23716 ms ✔ + [java] │ │ ├─ testNormalDistribution() 13767 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 14169 ms ✔ [java] │ ├─ BinaryCovarionModelTest ✔ [java] │ │ └─ testEquilibriumFrequencies() ✔ [java] │ ├─ BactrianUpDownOperatorTest ✔ [java] │ │ ├─ testNormalDistribution() ✔ - [java] │ │ └─ testLogNormalDistribution() 65078 ms ✔ + [java] │ │ └─ testLogNormalDistribution() 38354 ms ✔ [java] │ ├─ TreeLikelihoodTest ✔ [java] │ │ ├─ testAminoAcidLikelihoodGIBlosum62() ✔ [java] │ │ ├─ testAscertainedJC69Likelihood() ✔ @@ -15609,7 +15645,7 @@ [java] │ ├─ CompoundParameterHelperTest ✔ [java] │ │ └─ testCompoundParameterHelper() ✔ [java] │ ├─ RandomTreeTest ✔ - [java] │ │ └─ testCoalescentTimes() 67873 ms ✔ + [java] │ │ └─ testCoalescentTimes() 44941 ms ✔ [java] │ ├─ TreeUtilsTest ✔ [java] │ │ └─ testSortTreeAlphabetically() ✔ [java] │ ├─ BirthDeathGernhard08ModelTest ✔ @@ -15668,7 +15704,7 @@ [java] │ └─ logNormalTest() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 505017 ms + [java] Test run finished after 304630 ms [java] [ 51 containers found ] [java] [ 0 containers skipped ] [java] [ 51 containers started ] @@ -15682,10 +15718,10 @@ [java] [ 207 tests successful ] [java] [ 0 tests failed ] [java] -[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null1446317793 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/junitreport/TESTS-TestSuites.xml to /tmp/null965508635 [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: 1902ms -[junitreport] Deleting: /tmp/null1446317793 +[junitreport] Transform time: 1393ms +[junitreport] Deleting: /tmp/null965508635 junit-integration: [java] @@ -15694,12 +15730,12 @@ [java] Loading package BEAST.app v2.7.6 BEAST.app v2.7.6 BEAST.base v2.7.6 [java] Testing 160 classes [java] Done! - [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus - [java] exception thrown - [java] Cannot read the array length because "" is null [java] Loading package BEAST.app v2.7.6 [java] Loading package BEAST.app v2.7.6 [java] Loading package BEAST.base v2.7.6 + [java] Test Nexus Examples in /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/examples/nexus + [java] exception thrown + [java] Cannot read the array length because "" is null [java] [java] [java] @@ -15725,7 +15761,7 @@ [java] │ └─ testMutualDependencyOfPackageDependencies() ↷ Needs the user dir, which is intentionally void on Debian buildds [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 2649 ms + [java] Test run finished after 1986 ms [java] [ 8 containers found ] [java] [ 0 containers skipped ] [java] [ 8 containers started ] @@ -15743,10 +15779,10 @@ [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/null576555336 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/integrationreport/TESTS-TestSuites.xml to /tmp/null220253577 [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: 707ms -[junitreport] Deleting: /tmp/null576555336 +[junitreport] Transform time: 561ms +[junitreport] Deleting: /tmp/null220253577 junit-xmlparsertest: [java] @@ -15759,7 +15795,7 @@ [java] │ └─ testClassMap() ✔ [java] └─ JUnit Vintage ✔ [java] - [java] Test run finished after 1140 ms + [java] Test run finished after 884 ms [java] [ 4 containers found ] [java] [ 0 containers skipped ] [java] [ 4 containers started ] @@ -15777,15 +15813,15 @@ [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/null1340219112 +[junitreport] Processing /build/reproducible-path/beast2-mcmc-2.7.6+dfsg/beastfx/build/xmlparserreport/TESTS-TestSuites.xml to /tmp/null391801716 [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: 412ms -[junitreport] Deleting: /tmp/null1340219112 +[junitreport] Transform time: 280ms +[junitreport] Deleting: /tmp/null391801716 junit: BUILD SUCCESSFUL -Total time: 8 minutes 44 seconds +Total time: 5 minutes 17 seconds make[1]: Leaving directory '/build/reproducible-path/beast2-mcmc-2.7.6+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -15823,12 +15859,14 @@ 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/25718/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/25718/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/15150 and its subdirectories -I: Current time: Wed May 1 21:27:06 -12 2024 -I: pbuilder-time-stamp: 1714642026 +I: removing directory /srv/workspace/pbuilder/25718 and its subdirectories +I: Current time: Thu May 2 23:36:18 +14 2024 +I: pbuilder-time-stamp: 1714642578