Diff of the two buildlogs: -- --- b1/build.log 2024-01-19 01:13:33.837475890 +0000 +++ b2/build.log 2024-01-19 01:14:34.511002017 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 18 13:11:54 -12 2024 -I: pbuilder-time-stamp: 1705626714 +I: Current time: Thu Feb 20 21:36:35 +14 2025 +I: pbuilder-time-stamp: 1740036995 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -29,51 +29,83 @@ dpkg-source: info: applying javadoc.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/15382/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/101371/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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 Feb 20 07:36 /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/101371/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/101371/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=8 ' - DISTRIBUTION='bookworm' - 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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.15(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=15 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='b14f5f4d76c345dab1986356e408503d' - 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='15382' - PS1='# ' - PS2='> ' + INVOCATION_ID=fc88114dacf44b26a537f17df8bf0a8e + 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=101371 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.ZwFIRAF3/pbuilderrc_anza --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZwFIRAF3/b1 --logfile b1/build.log jebl2_0.1+git20201011.969bd4b-1.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.ZwFIRAF3/pbuilderrc_PcDo --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZwFIRAF3/b2 --logfile b2/build.log jebl2_0.1+git20201011.969bd4b-1.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 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash @@ -131,15 +163,15 @@ -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 22308 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 20 07:36 sh -> /bin/bash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar - -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 13860 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server @@ -159,7 +191,7 @@ -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew -I: user script /srv/workspace/pbuilder/15382/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/101371/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -425,7 +457,7 @@ Get: 216 http://deb.debian.org/debian bookworm/main i386 javahelper all 0.78 [97.2 kB] Get: 217 http://deb.debian.org/debian bookworm/main i386 libtrove-java all 2.1.0-3 [709 kB] Get: 218 http://deb.debian.org/debian bookworm/main i386 libtrove-java-doc all 2.1.0-3 [530 kB] -Fetched 244 MB in 19s (12.7 MB/s) +Fetched 244 MB in 5s (48.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 18156 files and directories currently installed.) @@ -1500,7 +1532,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/ && 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 > ../jebl2_0.1+git20201011.969bd4b-1_source.changes +I: user script /srv/workspace/pbuilder/101371/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/101371/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/ && 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 > ../jebl2_0.1+git20201011.969bd4b-1_source.changes dpkg-buildpackage: info: source package jebl2 dpkg-buildpackage: info: source version 0.1+git20201011.969bd4b-1 dpkg-buildpackage: info: source distribution unstable @@ -1561,7 +1597,7 @@ dist: BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 3 seconds ant -buildfile javadoc.xml Buildfile: /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/javadoc.xml @@ -1921,126 +1957,132 @@ [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/util/package-tree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/constant-values.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/serialized-form.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SequenceAlignmentsDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SystemOut.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWaterman.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpace.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/OverlapAlign.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NonOverlapMultipleLocalAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpaceAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/Align.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SequenceAlignmentsDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/AlignCommand.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SequenceShuffler.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/MultipleAligner.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/Align.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/BartonSternberg.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunsch.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/ProfileCharacter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWaterman.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SystemOut.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/OldNeedlemanWunschAffine.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/Traceback.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpaceAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SequenceShuffler.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NonOverlapMultipleLocalAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/TracebackPlotter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/Output.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/AlignmentTreeBuilderFactory.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/AlignmentTreeBuilderFactory.Result.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpaceAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpace.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/MaximalSegmentPair.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpaceAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpace.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/PairwiseAligner.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/PairwiseAligner.Result.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpace.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/OldNeedlemanWunschAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/MaximalSegmentPair.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunsch.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/Output.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/TracebackPlotter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/ProfileCharacter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/NeedlemanWunschAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/BartonSternberg.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/class-use/MultipleAligner.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam120.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/NucleotideScores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum80.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam170.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam220.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum65.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum45.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam110.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum70.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/AminoAcidScores.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam250.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam160.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum50.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/JukesCantor.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam240.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Scores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/ScoresFactory.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/ScoreMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam170.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum75.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Hamming.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam240.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam200.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum55.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum60.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/JukesCantor.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam190.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam130.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam140.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/ScoresFactory.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum80.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum90.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam220.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam100.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum60.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum70.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam210.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam180.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum50.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam250.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam230.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/ScoreMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum65.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam150.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum85.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam160.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/AminoAcidScores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum90.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam210.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/SubstScoreMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam190.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam100.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/NucleotideScores.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum55.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Blosum62.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam200.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Hamming.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam120.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam140.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam110.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/align/scores/class-use/Pam150.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/aligners/class-use/Aligner.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/ResampledAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/Patterns.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/BootstrappedAlignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/Alignment.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/BasicAlignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/JackknifedAlignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/Patterns.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/Pattern.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/JackknifedAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/ResampledAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/Alignment.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/alignments/class-use/ConsensusSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/CharacterType.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/ContinuousCharacter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/Character.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/DiscreteCharacter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/Character.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/characters/class-use/CharacterType.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/Coalescent.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/Expansion.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/Intervals.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ConstantPopulation.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ExponentialGrowth.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/LogisticGrowth.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/Coalescent.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/IntervalList.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/IntervalList.Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/IntervalList.IntervalType.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/EmpiricalDemographicFunction.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ConstExponential.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/Expansion.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/DemographicFunction.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/DemographicFunction.Utils.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ExponentialGrowth.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ConstLogistic.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/CataclysmicDemographic.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ConstExponential.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/ExponentialLogistic.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/JukesCantorDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/EmpiricalDemographicFunction.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/coalescent/class-use/CataclysmicDemographic.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/HKYDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/F84DistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/TamuraNeiDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/ModelBasedDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/BasicDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/DistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/JukesCantorDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/TamuraNeiDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/CannotBuildDistanceMatrixException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Utils.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/DistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/F84DistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/distances/class-use/BasicDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Edge.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Node.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Graph.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Graph.Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Graph.NoEdgeException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Edge.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/PHYLIPExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/FastaImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.Triangle.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/AlignmentImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NewickExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/graphs/class-use/Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/TreeImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/MEGAExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/TreeExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/FastaExporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ByteBuilder.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/AlignmentExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NewickExporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NexusImporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NexusImporter.MissingBlockException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NexusImporter.NexusBlock.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/TreeExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/PhylipSequentialImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/TabDelimitedImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/PHYLIPExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/AlignmentImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/FastaExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImmediateSequenceImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImmediateSequenceImporter.Callback.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/SequenceExporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NewickImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NexusExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/SequenceImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.Triangle.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/MEGAExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportHelper.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.UnknownTaxonException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.DuplicateTaxaException.html... @@ -2050,131 +2092,125 @@ [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.UnparsableDataException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.BadFormatException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportException.DuplicateFieldException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImportHelper.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImmediateSequenceImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/ImmediateSequenceImporter.Callback.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/AlignmentExporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/IllegalCharacterPolicy.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/PhylipSequentialImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/SequenceExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/NexusExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/TabDelimitedImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/SequenceImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/parsimony/class-use/FitchParsimony.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/io/class-use/FastaImporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/parsimony/class-use/ParsimonyCriterion.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/parsimony/class-use/FitchParsimony.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Codons.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/BasicSequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/CodonSequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/GaplessSequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/AminoAcids.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/StateClassification.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/StateClassification.Default.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/State.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/AminoAcidState.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/TranslatedSequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Sequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/NucleotideState.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Nucleotides.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/FilteredSequence.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/SequenceStateException.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Sequences.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/CodonSequence.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/SequenceType.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/SequenceType.Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/FilteredSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Sequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/State.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/StateClassification.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/StateClassification.Default.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Sequences.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/SequenceStateException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/AminoAcids.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/SequenceTester.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/Codons.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/BasicSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/NucleotideState.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/CanonicalSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/GaplessSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/AminoAcidState.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/CodonState.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/sequences/class-use/GeneticCode.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/AbstractRateMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/MatrixExponential.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/AminoAcidModel.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/RateMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/WAG.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/AminoAcidModel.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/substmodel/class-use/MatrixExponential.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/taxa/class-use/Taxon.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/taxa/class-use/MissingTaxonException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/taxa/class-use/TaxonomicLevel.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/BilleraMetric.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/RobinsonsFouldMetric.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/CladeHeightMetric.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/RootedTreeMetric.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBiPartitionInfo.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBiPartitionInfo.DistanceNorm.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedTreeUtils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SimpleRootedTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TransformedRootedTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TransformedRootedTree.Transform.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/Tree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/BaseEdge.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/MostProbableTopology.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/RobinsonsFouldMetric.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treemetrics/class-use/BilleraMetric.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/FilteredRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/CompactRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/CladeSystem.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SplitSystem.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ClusteringTreeBuilder.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedFromUnrooted.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeChangeEvent.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/NeighborJoiningTreeBuilder.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/BaseNode.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SplitSystem.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeSelectionChangeEvent.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SimpleTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedSubtree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/CalculateSplitRates.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SortedRootedTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SortedRootedTree.BranchOrdering.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeSelectionChangeEvent.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SplitUtils.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBiPartitionInfo.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBiPartitionInfo.DistanceNorm.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedTree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBuilder.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ReRootedTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ReRootedTree.RootingType.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/FilteredRootedTree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/AttributedCladeSystem.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SplitUtils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/CompactRootedTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SimpleTree.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/NeighborJoiningTreeBuilder.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ConsensusTreeBuilder.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ConsensusTreeBuilder.Method.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedSubtree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBuilderFactory.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBuilderFactory.ConsensusMethod.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBuilderFactory.DistanceModel.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeBuilderFactory.Method.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/MutableRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TransformedRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TransformedRootedTree.Transform.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/BaseEdge.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedTreeUtils.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/MostProbableTopology.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SimpleRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SortedRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/SortedRootedTree.BranchOrdering.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/RootedFromUnrooted.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeChangeListener.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/CladeSystem.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/Tree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/MutableRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ReRootedTree.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/ReRootedTree.RootingType.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/trees/class-use/TreeChangeEvent.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treesimulation/class-use/TreeSimulator.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/treesimulation/class-use/IntervalGenerator.html... 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[javadoc] Generating /build/reproducible-path/jebl2-0.1+git20201011.969bd4b/doc/jebl/evolution/aligners/package-use.html... @@ -2206,7 +2242,7 @@ [javadoc] 11 warnings BUILD SUCCESSFUL -Total time: 7 seconds +Total time: 4 seconds make[1]: Leaving directory '/build/reproducible-path/jebl2-0.1+git20201011.969bd4b' dh_auto_test create-stamp debian/debhelper-build-stamp @@ -2239,12 +2275,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/101371/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/101371/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/15382 and its subdirectories -I: Current time: Thu Jan 18 13:13:33 -12 2024 -I: pbuilder-time-stamp: 1705626813 +I: removing directory /srv/workspace/pbuilder/101371 and its subdirectories +I: Current time: Thu Feb 20 21:37:33 +14 2025 +I: pbuilder-time-stamp: 1740037053