Diff of the two buildlogs: -- --- b1/build.log 2024-04-13 11:40:14.134291747 +0000 +++ b2/build.log 2024-04-13 11:49:37.566750903 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 12 23:31:46 -12 2024 -I: pbuilder-time-stamp: 1713007906 +I: Current time: Sun Apr 14 01:40:30 +14 2024 +I: pbuilder-time-stamp: 1713008430 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying javadoc.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1741/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/10776/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +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 Apr 13 11:40 /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/10776/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/10776/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='08a54032ca224caf9e3e3f6e5ce0e6ae' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1741' - PS1='# ' - PS2='> ' + INVOCATION_ID=639156c08c964d219da0fa12255eeac1 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=10776 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.rwMZWJbv/pbuilderrc_WiEH --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.rwMZWJbv/b1 --logfile b1/build.log jebl2_0.1+git20230701.b3c0f25-1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.rwMZWJbv/pbuilderrc_TElL --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.rwMZWJbv/b2 --logfile b2/build.log jebl2_0.1+git20230701.b3c0f25-1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 10 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1741/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/10776/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -342,7 +374,7 @@ Get: 220 http://deb.debian.org/debian trixie/main armhf javahelper all 0.79 [84.6 kB] Get: 221 http://deb.debian.org/debian trixie/main armhf libtrove-java all 2.1.0-3 [709 kB] Get: 222 http://deb.debian.org/debian trixie/main armhf libtrove-java-doc all 2.1.0-3 [530 kB] -Fetched 218 MB in 6s (38.4 MB/s) +Fetched 218 MB in 12s (18.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19635 files and directories currently installed.) @@ -1068,8 +1100,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Apr 13 11:37:30 UTC 2024. -Universal Time is now: Sat Apr 13 11:37:30 UTC 2024. +Local time is now: Sat Apr 13 11:44:36 UTC 2024. +Universal Time is now: Sat Apr 13 11:44:36 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.10-3) ... @@ -1447,7 +1479,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/ && 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+git20230701.b3c0f25-1_source.changes +I: user script /srv/workspace/pbuilder/10776/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/10776/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/ && 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+git20230701.b3c0f25-1_source.changes dpkg-buildpackage: info: source package jebl2 dpkg-buildpackage: info: source version 0.1+git20230701.b3c0f25-1 dpkg-buildpackage: info: source distribution unstable @@ -1508,7 +1544,7 @@ dist: BUILD SUCCESSFUL -Total time: 25 seconds +Total time: 1 minute 8 seconds ant -buildfile javadoc.xml Buildfile: /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/javadoc.xml @@ -1868,122 +1904,121 @@ [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/util/package-tree.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/constant-values.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/serialized-form.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpaceAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunsch.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SystemOut.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/TracebackPlotter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SmithWaterman.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/ProfileCharacter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/MaximalSegmentPair.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Output.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NonOverlapMultipleLocalAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/OverlapAlign.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Align.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SequenceAlignmentsDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/OldNeedlemanWunschAffine.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SequenceShuffler.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Traceback.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpace.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/PairwiseAligner.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/PairwiseAligner.Result.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpaceAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NonOverlapMultipleLocalAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/OverlapAlign.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SequenceAlignmentsDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/MaximalSegmentPair.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpace.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/OldNeedlemanWunschAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Align.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/MultipleAligner.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SmithWatermanLinearSpaceAffine.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunsch.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/BartonSternberg.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Traceback.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/Output.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/AlignCommand.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/AlignmentTreeBuilderFactory.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/AlignmentTreeBuilderFactory.Result.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/SmithWaterman.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/TracebackPlotter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpaceAffine.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/NeedlemanWunschLinearSpace.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/MultipleAligner.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/class-use/AlignCommand.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam170.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam200.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum70.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/AminoAcidScores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum62.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam190.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam230.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum50.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam150.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum70.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam100.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/SubstScoreMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum85.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/NucleotideScores.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam160.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum80.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/ScoreMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Scores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam250.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum60.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam180.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum75.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/SubstScoreMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam220.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum90.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/ScoresFactory.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum65.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum75.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam170.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam240.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum62.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/ScoreMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam120.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Hamming.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam220.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam210.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam150.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam120.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/AminoAcidScores.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum45.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam200.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/JukesCantor.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam190.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum80.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam140.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam110.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam100.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum55.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam130.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum65.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/NucleotideScores.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum90.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/JukesCantor.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum85.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam240.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam230.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum55.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Blosum60.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam110.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/align/scores/class-use/Pam250.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/aligners/class-use/Aligner.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/Patterns.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/ConsensusSequence.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/BasicAlignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/JackknifedAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/Pattern.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/BootstrappedAlignment.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/ResampledAlignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/Pattern.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/JackknifedAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/BasicAlignment.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/ConsensusSequence.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/alignments/class-use/Alignment.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/characters/class-use/ContinuousCharacter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/characters/class-use/DiscreteCharacter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/characters/class-use/ContinuousCharacter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/characters/class-use/CharacterType.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/characters/class-use/Character.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ConstLogistic.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.IntervalType.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/LogisticGrowth.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ExponentialLogistic.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/Coalescent.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/CataclysmicDemographic.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ExponentialGrowth.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ConstantPopulation.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/CataclysmicDemographic.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ConstLogistic.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/DemographicFunction.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/DemographicFunction.Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/EmpiricalDemographicFunction.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/Intervals.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ExponentialGrowth.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ExponentialLogistic.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/LogisticGrowth.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.Utils.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/IntervalList.IntervalType.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/Expansion.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/ConstExponential.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/ModelBasedDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/JukesCantorDistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/EmpiricalDemographicFunction.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/coalescent/class-use/Coalescent.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/CannotBuildDistanceMatrixException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/HKYDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/DistanceMatrix.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/ModelBasedDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/F84DistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/TamuraNeiDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/BasicDistanceMatrix.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Utils.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Edge.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Node.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/distances/class-use/JukesCantorDistanceMatrix.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Graph.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Graph.Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Graph.NoEdgeException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NexusExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/IllegalCharacterPolicy.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/SequenceImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/SequenceExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/AlignmentExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/FastaExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TreeExporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TreeImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Node.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Edge.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/graphs/class-use/Utils.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/AlignmentImporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ByteBuilder.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NewickImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/PHYLIPExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NexusImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NexusImporter.MissingBlockException.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NexusImporter.NexusBlock.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/IllegalCharacterPolicy.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/NexusExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TreeExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/MEGAExporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TabDelimitedImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/PhylipSequentialImporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.UnknownTaxonException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.DuplicateTaxaException.html... @@ -1993,135 +2028,136 @@ [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.UnparsableDataException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.BadFormatException.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportException.DuplicateFieldException.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/FastaImporter.html... - [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TabDelimitedImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/FastaExporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/DistanceMatrixImporter.Triangle.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/TreeImporter.html... + [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImportHelper.html... [javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/io/class-use/ImmediateSequenceImporter.html... 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[javadoc] Generating /build/reproducible-path/jebl2-0.1+git20230701.b3c0f25/doc/jebl/evolution/aligners/package-use.html... @@ -2153,7 +2189,7 @@ [javadoc] 11 warnings BUILD SUCCESSFUL -Total time: 29 seconds +Total time: 1 minute 20 seconds make[1]: Leaving directory '/build/reproducible-path/jebl2-0.1+git20230701.b3c0f25' dh_auto_test create-stamp debian/debhelper-build-stamp @@ -2186,12 +2222,14 @@ 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/10776/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/10776/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/1741 and its subdirectories -I: Current time: Fri Apr 12 23:40:08 -12 2024 -I: pbuilder-time-stamp: 1713008408 +I: removing directory /srv/workspace/pbuilder/10776 and its subdirectories +I: Current time: Sun Apr 14 01:49:31 +14 2024 +I: pbuilder-time-stamp: 1713008971