Diff of the two buildlogs: -- --- b1/build.log 2025-01-02 14:45:45.818872456 +0000 +++ b2/build.log 2025-01-02 14:50:31.573858872 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 2 02:40:18 -12 2025 -I: pbuilder-time-stamp: 1735828818 +I: Current time: Fri Jan 3 04:45:59 +14 2025 +I: pbuilder-time-stamp: 1735829159 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,52 +28,84 @@ dpkg-source: info: applying fix_encoding.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/20411/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/D01_modify_environment starting +debug: Running on virt64b. +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 Jan 2 14:46 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='0806f49a8b9641a0bdafb4e09143dd53' - 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='20411' - PS1='# ' - PS2='> ' + INVOCATION_ID=dbd518b0a9cb4354b969c1cdd66500f9 + 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=13390 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.cnLJolEK/pbuilderrc_j1KY --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cnLJolEK/b1 --logfile b1/build.log libpal-java_1.5.1+dfsg-9.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.cnLJolEK/pbuilderrc_LKFw --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.cnLJolEK/b2 --logfile b2/build.log libpal-java_1.5.1+dfsg-9.dsc' + SUDO_GID=113 + SUDO_UID=107 + 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 6.1.0-28-armmp-lpae #1 SMP Debian 6.1.119-1 (2024-11-22) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/20411/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -365,7 +397,7 @@ Get: 246 http://deb.debian.org/debian trixie/main armhf fastjar armhf 2:0.98-7 [43.9 kB] Get: 247 http://deb.debian.org/debian trixie/main armhf jarwrapper all 0.80 [9692 B] Get: 248 http://deb.debian.org/debian trixie/main armhf javahelper all 0.80 [80.4 kB] -Fetched 222 MB in 8s (27.8 MB/s) +Fetched 222 MB in 6s (39.3 MB/s) Preconfiguring packages ... 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 ... 19679 files and directories currently installed.) @@ -1200,8 +1232,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Jan 2 14:43:07 UTC 2025. -Universal Time is now: Thu Jan 2 14:43:07 UTC 2025. +Local time is now: Thu Jan 2 14:48:11 UTC 2025. +Universal Time is now: Thu Jan 2 14:48:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:armhf (1.17.0-2+b1) ... @@ -1608,7 +1640,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libpal-java-1.5.1+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 > ../libpal-java_1.5.1+dfsg-9_source.changes +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libpal-java-1.5.1+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 > ../libpal-java_1.5.1+dfsg-9_source.changes dpkg-buildpackage: info: source package libpal-java dpkg-buildpackage: info: source version 1.5.1+dfsg-9 dpkg-buildpackage: info: source distribution unstable @@ -1775,7 +1811,7 @@ [jar] Building jar: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/lib/pal-cvs.jar BUILD SUCCESSFUL -Total time: 20 seconds +Total time: 19 seconds ant -buildfile src/build.xml -propertyfile debian/ant.properties doc Buildfile: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml @@ -2601,107 +2637,105 @@ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/constant-values.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/serialized-form.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/GeneralObjectState.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Markable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Assessor.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StateProvider.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ProbabilityIterator.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Markable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Ranker.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/SearchEngine.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ObjectState.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/Assessor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/UndoableAction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/UndoableAction.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StateProvider.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/StoppingCriteria.Factory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/Alignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/ObjectState.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/class-use/SearchEngine.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/MultiLocusAnnotatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignmentOld.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AbstractAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleCharacterAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/IndelAnnotatedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAnnotatedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/IndelAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/GapBalancedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AbstractAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/Genotype.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/CharacterAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/BootstrappedAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignmentOld.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AnnotationAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ReadAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAnnotatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.PhylipClustalAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReaders.UnalignedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/IndelAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AnnotationAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.BucketReceiver.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentReceiver.SingleReceiver.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/StrippedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentBuilder.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/BootstrappedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/JumbledAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentGenerator.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/DataTranslator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAnnotatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SitePattern.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleCharacterAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/MultiLocusAnnotatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/Alignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAnnotatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/DataTranslator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentParseException.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/SimpleAlignment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicClockTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SkylinePlot.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/IntervalsExtractor.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpGrowth.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentIntervals.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpConst.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/AlignmentTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/class-use/ConcatenatedAnnotatedAlignment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ExponentialGrowth.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentIntervals.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpGrowth.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/IntervalsExtractor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentSimulator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstExpConst.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.Results.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentException.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentSimulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ExpandingPopulation.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ConstantPopulation.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/ExponentialGrowth.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/DemographicClockTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SerialCoalescentGenerator.Results.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/CoalescentTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACNucleotides.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/SpecificAminoAcids.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACPenaltyTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/class-use/SkylinePlot.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/Nucleotides.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/AminoAcids.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/Codons.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableFactory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/NumericDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataTypeTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TransitionPenaltyTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACPenaltyTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/Codons.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/SpecificAminoAcids.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/SimpleDataType.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TwoStates.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/AmbiguousDataType.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/NumericDataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/StateRemover.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TransitionPenaltyTable.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/GapBalanced.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataType.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/DataType.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/GapBalanced.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableFactory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/CodonTableUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/ReadDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/AmbiguousDataType.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/MolecularDataType.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/IUPACNucleotides.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/datatype/class-use/TwoStates.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/PairwiseDistance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/AlignmentDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/PairwiseDistance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/JukesCantorDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceParseException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/ReadDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/SequencePairLikelihood.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLeafCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleModelFastFourStateLHCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceParseException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixAccess.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/distance/class-use/DistanceMatrixGenerator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.HeightConverter.html... @@ -2709,10 +2743,6 @@ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/MolecularClockLikelihoodModel.External.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLHCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.AbstractExternal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Generator.html... @@ -2720,240 +2750,239 @@ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.External.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLeafCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodSummary.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicLikelihoodValue.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ConditionalProbabilityStore.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ConditionalProbabilityStore.ExtraProcessor.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastFourStateLHCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ModelParameters.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/PatternInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ChiSquareValue.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicLikelihoodValue.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleModelFastFourStateLHCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastLikelihoodCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/ModelParameters.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/GeneralLikelihoodCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLHCalculator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleMolecularClockLikelihoodModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodOptimiser.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/PatternInfo.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SingleSplitMolecularClockLikelihoodModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodSummary.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/DemographicValue.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.LeafImpl.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleUnconstrainedLikelihoodModel.InternalImpl.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastLikelihoodCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLikelihoodCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SiteDetails.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Instance.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Leaf.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.Internal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/UnconstrainedLikelihoodModel.External.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/SimpleLikelihoodCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/GeneralLikelihoodCalculator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainter.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/PositionedNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/FastFourStateLHCalculator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LikelihoodTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LabelDisplayer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LabelDisplayer.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LayoutTracker.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreeComponent.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterNormal.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LinkageDisequilibriumComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/CircularGraphics.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterCircular.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/NameColouriser.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainter.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/Painter.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusTokenizer.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/InputSource.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreeComponent.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterCircular.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/PositionedNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/TreePainterNormal.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/gui/class-use/LayoutTracker.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/FormattedInput.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusParseException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/InputSource.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/OutputTarget.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusParseException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/NexusTokenizer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/io/class-use/FormattedOutput.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/BoundsCheckedFunction.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/EvaluationCounter.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UnivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ConjugateDirectionSearch.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.OEFactory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MathUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UnivariateMinimum.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MFWithGradient.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.RoundOptimiser.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/Matrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateMinimum.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateMinimum.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MersenneTwisterFast.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GammaFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LineFunction.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/Binomial.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ErrorFunction.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UrnModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MultivariateFunction.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GeneralizedDEOptimizer.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalLineFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MachineAccuracy.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MinimiserMonitor.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MinimiserMonitor.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MachineAccuracy.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/DifferentialEvolution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GammaFunction.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalSearch.RoundOptimiser.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UnivariateFunction.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ConjugateGradientSearch.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MersenneTwisterFast.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/Matrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MFWithGradient.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/DifferentialEvolution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/EvaluationCounter.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/NumericalDerivative.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/MathUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/UrnModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ErrorFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/BoundsCheckedFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/GeneralizedDEOptimizer.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalHints.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalHints.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/NumericalDerivative.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LineFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrderEnumerator.OEFactory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/ConjugateGradientSearch.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/LMSSolver.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalLineFunction.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/WindowedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/DeltaModel.Instance.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/SteppedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/ConstantMutationRate.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/WindowedMutationRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/MutationRateModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/MutationRateModel.Factory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/mep/class-use/SteppedMutationRate.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.Relabeller.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectEvent.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.Factory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NeoParameterized.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Attribute.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedDoubleBundle.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/UnitsProvider.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterEvent.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedNeoWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.Null.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.ParameterizedBase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Parameterized.ParameterizedUser.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeOrderCharacterData.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MutableDouble.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ExternalParameterListener.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalEventMulticaster.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ReleaseInfo.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SimpleIdGroup.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Summarizable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NamedParameterized.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGroup.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGroup.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Listener.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NeoParameterized.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGenerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TOCDSampleInformation.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeStamp.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Report.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Identifier.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectEvent.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ExternalParameterListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SimpleSummarizable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Units.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/BranchLimits.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.ParameterAccessWatcher.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TableReport.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Attribute.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectListener.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalObjectListener.EventGenerator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Nameable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IndividualParameterHandler.Listener.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TableReport.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/BranchLimits.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Units.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/IdGroup.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ReleaseInfo.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/UnitsProvider.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MultiParameterized.ParameterAccessWatcher.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/NamedParameterized.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Report.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SampleInformation.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Identifier.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TOCDSampleInformation.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/MutableDouble.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/SimpleIdGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterEvent.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedNeoWrapper.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeOrderCharacterData.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/LabelMapping.Relabeller.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/PalEventMulticaster.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/ParameterizedDoubleBundle.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/misc/class-use/TimeStamp.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/popgen/class-use/LinkageDisequilibrium.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ChiSquareDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ShimodairaHasegawaTest.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodRatioTest.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/DiscreteStatistics.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ExponentialDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/GammaDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/NormalDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/GeneralTopologyPool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/PenalizedLikelihood.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/TopologyTestEngine.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/TopologyTestEngine.StatisticsHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/TopologyTestEngine.TopologyPool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/TopologyTestEngine.TestResult.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ParetoDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/BootstrapStatistics.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ShimodairaHasegawaStatistics.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/PenalizedLikelihood.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ExponentialDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/GammaDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/FisherExact.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/KishinoHasegawaTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ChiSquareTest.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/BootstrapStatistics.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/DiscreteStatistics.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ChiSquareDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodRatioTest.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ShimodairaHasegawaTest.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/RELLTopologyPool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ContigencyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ReplicateLikelihoodEvaluator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ReplicateLikelihoodEvaluator.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ContigencyTable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodEvaluator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodEvaluator.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodEvaluator.SimpleMLResult.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/LikelihoodEvaluator.MLResult.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/NormalDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/FisherExact.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ModelSupport.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/KishinoHasegawaTest.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/MatrixExponential.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SingleClassSubstitutionModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AbstractRateMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/ClassDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TN.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ShimodairaHasegawaStatistics.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/statistics/class-use/ParetoDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/HKY.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/F84.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/ConstantIndependentSingleSplitDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NucleotideModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/F81.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AminoAcidModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GammaRates.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GeneralPoissonRateMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/InvariableSites.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/PositiveSelectionRateMatrixGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SimpleRateMatrixGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CachedRateMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TransitionProbability.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TwoStateModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionModel.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SaturatedSingleSplitDistribution.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/VariableIndependentSingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NeoRateMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GeneralRateDistributionSubstitutionModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/VT.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SequenceSimulator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/UniformRate.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AminoAcidModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/MTREV24.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NucleotideModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/ClassDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/YangCodonModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/YangCodonModel.SimpleNeutralSelection.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/YangCodonModel.SimplePositiveSelection.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/YangCodonModel.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CPREV.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GeneralPoissonRateMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/InvariableSites.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GTR.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/UniformRate.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/BLOSUM62.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/WAG.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TwoStateModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SingleSplitDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/HKY.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/PositiveSelectionRateMatrixGroup.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CodonModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SequenceSimulator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixGroup.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SaturatedSingleSplitDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixHandler.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/MultiRateMatrixHandler.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NeutralSelectionRateMatrixGroup.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AminoAcidModelID.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TN.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/Dayhoff.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GeneralREVRateMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/VT.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CodonModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SingleSplitDistribution.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TemporalModelChange.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TemporalModelChange.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/TransitionProbability.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionModel.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SingleClassSubstitutionModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/MultiRateMatrixHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/JTT.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GeneralRateDistributionSubstitutionModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CachedRateMatrix.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/VariableIndependentSingleSplitDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/ConstantIndependentSingleSplitDistribution.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/Dayhoff.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SimpleRateMatrixGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/SubstitutionTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/MatrixExponential.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixHandler.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/WAG.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/CPREV.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/RateMatrixGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NeutralSelectionRateMatrixGroup.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AminoAcidModelID.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/NucleotideModelID.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMADistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/AbstractRateMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/F81.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GammaRates.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/substmodel/class-use/GTR.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/RateHandler.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/RateHandler.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMATree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/ThetaHandler.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/ThetaHandler.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMATree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMADistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMABase.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMABase.CISummary.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/SUPGMABase.PopulationParameters.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/RateHandler.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/supgma/class-use/RateHandler.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ReadTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimpleTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SplitSystem.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/AttributeNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimulatedAlignment.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimulatedAlignment.Factory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeRestricter.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Tree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Tree.TreeBase.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Local.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/AttributeNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SplitSystem.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ClockTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ReadTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.BaseBranch.html... @@ -2961,96 +2990,103 @@ [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.GeneralBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.UNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnrootedTreeInterface.Instructee.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Tree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Tree.TreeBase.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/LogParameterizedTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnconstrainedTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Node.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeRestricter.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeFactory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Local.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/CladeSystem.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/MutationRateModelTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimpleNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ClockTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeIterator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeManipulator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeManipulator.PALNodeWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeManipulator.PALBranchWrapper.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeManipulator.BranchAccess.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SplitUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/MutationRateModelTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeTool.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UPGMATree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NodeFactory.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/Node.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/CladeSystem.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NeighborJoiningTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeParseException.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeOperation.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ClusterTree.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ClusterTree.ClusteringMethod.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeIterator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/UnconstrainedTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/LogParameterizedTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.ParameterizedTreeBase.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.Utils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.RBranch.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.RNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/RootedTreeInterface.Instructee.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimpleTree.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SimpleNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeGenerator.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/SplitUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.ParameterizedTreeBase.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/ParameterizedTree.Factory.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/NeighborJoiningTree.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeParseException.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/tree/class-use/TreeUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SRDTGlobalClockModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralTreeComponent.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedLeafNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/RootAccess.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GlobalClockModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/TreeSearchTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FixedBSRDTGlobalClockModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeLeafNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/Constants.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.HeightAdjustment.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/HeightInformationUser.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedInternalNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractLeafNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ParentableConstrainedNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractParentableConstrainedNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnrootedMLSearcher.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnrootedMLSearcher.StateObject.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstructionTool.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearcherUtils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralTreeComponent.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/HeightInformationUser.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.GroupManager.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SRDTGlobalClockModel.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/PivotNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralOptimisable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ParentableConstrainedNode.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/NodeAccess.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnconstrainedModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralLikelihoodSearcher.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstructionTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GlobalClockModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeLeafNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.LikelihoodScoreAccess.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralConstraintGroupManager.Store.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GroupLeader.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralLikelihoodSearcher.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/Constants.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FixedSRDTGlobalClockModel.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedNode.HeightAdjustment.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractParentableConstrainedNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/MRDTGlobalClockModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/TreeSearchTool.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstraintModel.GroupManager.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeBranch.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/ConstrainedInternalNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/NodeAccess.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/UnconstrainedModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearchMonitor.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FixedBSRDTGlobalClockModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/SearcherUtils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/RootAccess.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeNode.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/FreeInternalNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/AbstractLeafNode.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Version.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GroupLeader.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/MRDTGlobalClockModel.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/BranchAccess.Utils.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/treesearch/class-use/GeneralOptimisable.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/XMLConstants.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Version.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/HeapSort.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DefaultCache.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ComparableDouble.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Comparator.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Logger.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Comparable.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKey.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKeyCache.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Log.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ThreeNumberSort.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Comparator.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/AlgorithmCallback.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/AlgorithmCallback.Utils.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Logger.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/Log.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKeyCache.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ThreeNumberSort.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/ComparableDouble.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DoubleKey.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/util/class-use/DefaultCache.html... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/XmlParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/ElementFactory.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/ElementParser.html... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/xml/class-use/XmlParseException.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/algorithmics/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/alignment/package-use.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/coalescent/package-use.html... @@ -3083,7 +3119,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 31 seconds +Total time: 30 seconds make[1]: Leaving directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -3119,12 +3155,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/13390/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/13390/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/20411 and its subdirectories -I: Current time: Thu Jan 2 02:45:40 -12 2025 -I: pbuilder-time-stamp: 1735829140 +I: removing directory /srv/workspace/pbuilder/13390 and its subdirectories +I: Current time: Fri Jan 3 04:50:26 +14 2025 +I: pbuilder-time-stamp: 1735829426