Diff of the two buildlogs: -- --- b1/build.log 2024-04-16 20:42:15.092511513 +0000 +++ b2/build.log 2024-04-16 20:43:31.605265186 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 16 08:40:16 -12 2024 -I: pbuilder-time-stamp: 1713300016 +I: Current time: Tue May 20 17:05:18 +14 2025 +I: pbuilder-time-stamp: 1747710318 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,54 +29,86 @@ 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/36954/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/67882/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 20 03:05 /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/67882/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/67882/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='210ff01cc3674ac285a47fdeacede48d' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='36954' - PS1='# ' - PS2='> ' + INVOCATION_ID=06e1c4254d5b4be6ba9340f2b22b9243 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=67882 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.egAw5b38/pbuilderrc_5lXl --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.egAw5b38/b1 --logfile b1/build.log libpal-java_1.5.1+dfsg-9.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.egAw5b38/pbuilderrc_vs6e --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.egAw5b38/b2 --logfile b2/build.log libpal-java_1.5.1+dfsg-9.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 16 11:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/36954/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 18 17:46 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/67882/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -337,7 +369,7 @@ Get: 215 http://deb.debian.org/debian trixie/main i386 fastjar i386 2:0.98-7 [47.3 kB] Get: 216 http://deb.debian.org/debian trixie/main i386 jarwrapper all 0.79 [10.1 kB] Get: 217 http://deb.debian.org/debian trixie/main i386 javahelper all 0.79 [84.6 kB] -Fetched 229 MB in 5s (47.2 MB/s) +Fetched 229 MB in 3s (69.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:i386. (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 ... 19874 files and directories currently installed.) @@ -1048,8 +1080,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Apr 16 20:41:17 UTC 2024. -Universal Time is now: Tue Apr 16 20:41:17 UTC 2024. +Local time is now: Tue May 20 03:05:51 UTC 2025. +Universal Time is now: Tue May 20 03:05:51 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.10-3) ... @@ -1422,7 +1454,11 @@ 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/67882/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/67882/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 @@ -1588,7 +1624,7 @@ [jar] Building jar: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/lib/pal-cvs.jar BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 5 seconds ant -buildfile src/build.xml -propertyfile debian/ant.properties doc Buildfile: /build/reproducible-path/libpal-java-1.5.1+dfsg/src/build.xml @@ -2416,141 +2452,123 @@ [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/StateProvider.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/Markable.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/SearchEngine.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/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/SearchEngine.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/StateProvider.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/ObjectState.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/alignment/class-use/ConcatenatedAlignment.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/StrippedAnnotatedAlignment.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/alignment/class-use/IndelAnnotatedAlignment.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/BootstrappedAlignment.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/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/alignment/class-use/AlignmentUtils.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/AlignmentBuilder.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/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/IndelAlignment.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/AnnotationAlignment.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/AlignmentBuilder.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/ReadAlignment.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/AnnotationAlignment.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/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/StrippedAlignment.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/ReadAlignmentOld.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/AbstractAlignment.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/JumbledAlignment.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/SimpleCharacterAlignment.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/Genotype.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/Alignment.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/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/BootstrappedAlignment.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/AlignmentParseException.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/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/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/AlignmentParseException.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/ConstExpGrowth.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/ConstExpConst.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/CoalescentTree.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/DemographicTree.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/IntervalsExtractor.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/SerialCoalescentSimulator.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/ConstExpGrowth.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/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/ExpandingPopulation.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/CoalescentSimulator.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/CoalescentIntervals.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/SkylinePlot.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/datatype/class-use/CodonTableFactory.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/Nucleotides.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/TransitionPenaltyTable.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/datatype/class-use/StateRemover.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/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/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/SpecificAminoAcids.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/DataTypeTool.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/CodonTable.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/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/AmbiguousDataType.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/NumericDataType.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/DataTypeTool.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/IUPACNucleotides.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/CodonTableUtils.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/distance/class-use/PairwiseDistance.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/TwoStates.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/distance/class-use/DistanceMatrix.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/DistanceTool.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/SequencePairLikelihood.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/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/DistanceParseException.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/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/AlignmentDistanceMatrix.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/eval/class-use/LikelihoodCalculator.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/distance/class-use/SequencePairLikelihood.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/GeneralLikelihoodCalculator.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/ChiSquareValue.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/LikelihoodValue.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/SimpleMolecularClockLikelihoodModel.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/SimpleLikelihoodCalculator.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... - [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Factory.html... - [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/ChiSquareValue.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/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/LikelihoodValue.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/SingleSplitMolecularClockLikelihoodModel.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/GeneralLikelihoodCalculator.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/FastLikelihoodCalculator.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/ModelParameters.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/DemographicLikelihoodValue.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/FastFourStateLHCalculator.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/LikelihoodSummary.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/SimpleMolecularClockLikelihoodModel.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... @@ -2558,202 +2576,225 @@ [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/gui/class-use/LinkageDisequilibriumComponent.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/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... + [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/eval/class-use/LHCalculator.Factory.html... + [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/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/LikelihoodTool.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/FastFourStateLHCalculator.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/LikelihoodOptimiser.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/SingleSplitMolecularClockLikelihoodModel.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/gui/class-use/TreeComponent.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/NameColouriser.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/CircularGraphics.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/gui/class-use/LayoutTracker.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/CircularGraphics.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/gui/class-use/TreePainterCircular.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/io/class-use/FormattedOutput.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/gui/class-use/LinkageDisequilibriumComponent.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/io/class-use/NexusTokenizer.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/FormattedInput.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/io/class-use/InputSource.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/LineFunction.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/NumericalDerivative.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/BoundsCheckedFunction.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/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/Binomial.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/GeneralizedDEOptimizer.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/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/MachineAccuracy.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/MultivariateFunction.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/DifferentialEvolution.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/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/Binomial.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/GammaFunction.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/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/EvaluationCounter.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/DifferentialEvolution.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/LineFunction.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/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/UrnModel.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/NumericalDerivative.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/ConjugateDirectionSearch.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/MathUtils.html... [javadoc] Generating /build/reproducible-path/libpal-java-1.5.1+dfsg/src/dist/doc/api/pal/math/class-use/OrthogonalHints.html... 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[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/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/WindowedMutationRate.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/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/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/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/BranchLimits.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/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... 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[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... @@ -2761,109 +2802,104 @@ [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... 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[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/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/AttributeNode.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/UPGMATree.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/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/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/SplitUtils.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/ClockTree.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/NodeFactory.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/MutationRateModelTree.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/AttributeNode.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/TreeRestricter.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/NodeFactory.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/ReadTree.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/TreeParseException.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/treesearch/class-use/GeneralLikelihoodSearcher.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/NodeAccess.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/AbstractParentableConstrainedNode.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/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/UnconstrainedModel.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/MRDTGlobalClockModel.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/PivotNode.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/ConstrainedInternalNode.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/ParentableConstrainedNode.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/FixedBSRDTGlobalClockModel.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/FreeNode.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/ConstrainedLeafNode.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/GeneralOptimisable.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/FreeBranch.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/NodeAccess.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/HeightInformationUser.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/Constants.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/PivotNode.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/ParentableConstrainedNode.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/FreeNode.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/FreeLeafNode.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/FixedBSRDTGlobalClockModel.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/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/RootAccess.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/Constants.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/util/class-use/Log.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/XMLConstants.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/DefaultCache.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/Logger.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/treesearch/class-use/ConstrainedLeafNode.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/UnconstrainedModel.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/GeneralTreeComponent.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/Logger.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/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/ComparableDouble.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/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/DefaultCache.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/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/Log.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/xml/class-use/ElementFactory.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... @@ -2895,7 +2931,7 @@ [javadoc] 100 warnings BUILD SUCCESSFUL -Total time: 13 seconds +Total time: 11 seconds make[1]: Leaving directory '/build/reproducible-path/libpal-java-1.5.1+dfsg' create-stamp debian/debhelper-build-stamp dh_prep @@ -2922,8 +2958,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'libpal-java' in '../libpal-java_1.5.1+dfsg-9_all.deb'. dpkg-deb: building package 'libpal-java-doc' in '../libpal-java-doc_1.5.1+dfsg-9_all.deb'. +dpkg-deb: building package 'libpal-java' in '../libpal-java_1.5.1+dfsg-9_all.deb'. dpkg-genbuildinfo --build=binary -O../libpal-java_1.5.1+dfsg-9_i386.buildinfo dpkg-genchanges --build=binary -O../libpal-java_1.5.1+dfsg-9_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2931,12 +2967,14 @@ 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/67882/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/67882/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/36954 and its subdirectories -I: Current time: Tue Apr 16 08:42:14 -12 2024 -I: pbuilder-time-stamp: 1713300134 +I: removing directory /srv/workspace/pbuilder/67882 and its subdirectories +I: Current time: Tue May 20 17:06:30 +14 2025 +I: pbuilder-time-stamp: 1747710390