Diff of the two buildlogs: -- --- b1/build.log 2024-01-12 06:04:44.785705689 +0000 +++ b2/build.log 2024-01-12 06:09:44.198666402 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jan 11 17:53:45 -12 2024 -I: pbuilder-time-stamp: 1705038826 +I: Current time: Fri Feb 14 02:27:50 +14 2025 +I: pbuilder-time-stamp: 1739449670 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -43,49 +43,81 @@ dpkg-source: info: applying adding_opens_arg_for_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/3177718/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/D01_modify_environment starting +debug: Running on ionos5-amd64. +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 13 12:27 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2185384/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 ' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='52135773089246859bca7e3eb645bb7b' - 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='3177718' - PS1='# ' - PS2='> ' + INVOCATION_ID=90f07de72062449cbc72b85daf4d0efc + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-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=2185384 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.g7IW0ol2/pbuilderrc_UPGC --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.g7IW0ol2/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-9.dsc' - SUDO_GID='111' - SUDO_UID='106' - 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.g7IW0ol2/pbuilderrc_1NPu --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.g7IW0ol2/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-9.dsc' + SUDO_GID=110 + SUDO_UID=105 + 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 ionos11-amd64 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 23 2023 bash @@ -143,15 +175,15 @@ -rwxr-xr-x 1 root root 52112 Sep 20 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 20 2022 rm -rwxr-xr-x 1 root root 56240 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 27560 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 27560 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 126424 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 13 12:27 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 20 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 20 2022 stty -rwsr-xr-x 1 root root 72000 Mar 23 2023 su -rwxr-xr-x 1 root root 39824 Sep 20 2022 sync -rwxr-xr-x 1 root root 531984 Apr 6 2023 tar - -rwxr-xr-x 1 root root 14520 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 14520 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 109616 Sep 20 2022 touch -rwxr-xr-x 1 root root 35664 Sep 20 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 2023 ulockmgr_server @@ -171,7 +203,7 @@ -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/3177718/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -717,7 +749,7 @@ Get: 428 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get: 429 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjava amd64 1.0-6-1+b1 [917 kB] Get: 430 http://deb.debian.org/debian bookworm/main amd64 testng all 6.9.12-4 [795 kB] -Fetched 381 MB in 1min 35s (4020 kB/s) +Fetched 381 MB in 4s (103 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (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 ... 18148 files and directories currently installed.) @@ -2099,8 +2131,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Jan 12 05:56:18 UTC 2024. -Universal Time is now: Fri Jan 12 05:56:18 UTC 2024. +Local time is now: Thu Feb 13 12:28:43 UTC 2025. +Universal Time is now: Thu Feb 13 12:28:43 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2656,7 +2688,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-9_source.changes +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-9_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-9 dpkg-buildpackage: info: source distribution unstable @@ -6203,14 +6239,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.080 s] -[INFO] Goby I/O ........................................... SUCCESS [01:09 min] -[INFO] Goby Full Distribution ............................. SUCCESS [01:17 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.057 s] +[INFO] Goby I/O ........................................... SUCCESS [ 26.718 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 29.254 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:27 min -[INFO] Finished at: 2024-01-11T17:59:10-12:00 +[INFO] Total time: 56.175 s +[INFO] Finished at: 2025-02-14T02:30:02+14:00 [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -6507,46 +6543,46 @@ [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 44592.1 for sample B-7 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 44895.1 for sample B-3 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 88396.7 for sample A-3 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89366.1 for sample A-12 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 44652.7 for sample B-15 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45319.2 for sample B-14 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45319.2 for sample B-11 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 90638.4 for sample A-17 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 43380.4 for sample B-2 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 46712.7 for sample B-10 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 90699.0 for sample A-16 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45803.9 for sample B-8 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45137.4 for sample B-4 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89547.8 for sample A-2 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89669.0 for sample A-0 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45258.6 for sample B-6 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89850.8 for sample A-9 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 91486.6 for sample A-8 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89790.2 for sample A-5 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 90274.9 for sample A-4 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 92213.7 for sample A-6 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 90880.7 for sample A-7 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45137.4 for sample B-5 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89729.6 for sample A-10 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 90941.3 for sample A-14 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45925.1 for sample B-9 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 93364.8 for sample A-1 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 44471.0 for sample B-0 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 46167.4 for sample B-12 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 46046.2 for sample B-13 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 91365.4 for sample A-19 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 88033.1 for sample A-18 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 91304.8 for sample A-15 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45985.7 for sample B-1 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 89729.6 for sample A-13 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 93001.3 for sample A-11 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 46349.2 for sample B-16 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45622.1 for sample B-17 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 44531.6 for sample B-19 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 45440.4 for sample B-18 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49806.6 for sample B-7 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47698.4 for sample B-3 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 95792.0 for sample A-3 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102117 for sample A-12 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49147.7 for sample B-15 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52112.4 for sample B-14 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48554.8 for sample B-11 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 101919 for sample A-17 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50794.8 for sample B-2 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48225.4 for sample B-10 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98427.3 for sample A-16 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48291.3 for sample B-8 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50399.5 for sample B-4 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98624.9 for sample A-2 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102841 for sample A-0 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48686.6 for sample B-6 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97504.9 for sample A-9 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99217.8 for sample A-8 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 95923.8 for sample A-5 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99086.1 for sample A-4 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97175.5 for sample A-6 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 96253.2 for sample A-7 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49279.5 for sample B-5 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100272 for sample A-10 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98822.6 for sample A-14 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49411.3 for sample B-9 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97768.4 for sample A-1 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48225.4 for sample B-0 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49411.3 for sample B-12 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48423.1 for sample B-13 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100535 for sample A-19 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99876.7 for sample A-18 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98624.9 for sample A-15 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49477.2 for sample B-1 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97900.2 for sample A-13 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100931 for sample A-11 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49806.6 for sample B-16 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48423.1 for sample B-17 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49477.2 for sample B-19 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48620.7 for sample B-18 Creating base test directory: test-results/stats-writer allele: A ref: [CC] alt: [T][main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value [main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. @@ -6611,7 +6647,7 @@ [ 49 [0.943789, 0.943789] ] element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B -[ id-1 [1.005510746257877, 0.49934982445410714, 0.007928500330585328, -1.0018772308658284, 0.0, 0.0] ] +[ id-1 [0.9953184599151038, 0.5006510400291034, -0.006769893822425353, -0.998122717478194, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 @@ -6646,10 +6682,10 @@ truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 truncated fdr=1.00000 original=1.00000 -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 15 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 15 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 15 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 15 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads. ##fileformat=VCFv4.1 ##Goby=UNKNOWN ##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, @@ -7529,202 +7565,196 @@ Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 -Appending count: 46341 length: 6 -Appending count: 8867 length: 2 -Appending count: 3291 length: 5 -Appending count: 35089 length: 7 -Appending count: 30920 length: 3 -Appending count: 17212 length: 2 -Appending count: 39002 length: 4 -Appending count: 49645 length: 10 -Appending count: 10038 length: 10 -Appending count: 32507 length: 4 -Appending count: 24973 length: 8 -Appending count: 49374 length: 8 -Appending count: 45950 length: 10 -Appending count: 14558 length: 6 -Appending count: 17558 length: 10 -Appending count: 42794 length: 4 -Appending count: 25202 length: 3 -Appending count: 10884 length: 6 -Appending count: 34997 length: 3 -Appending count: 39705 length: 10 -Appending count: 16021 length: 2 -Appending count: 27582 length: 9 -Appending count: 4895 length: 2 -Appending count: 4247 length: 1 -Appending count: 6571 length: 1 -Appending count: 37985 length: 6 -Appending count: 36090 length: 5 -Appending count: 12335 length: 8 -Appending count: 41483 length: 7 -Appending count: 42642 length: 4 - position= 0 count= 46341 - position= 1 count= 46341 - position= 2 count= 46341 - position= 3 count= 46341 - position= 4 count= 46341 - position= 5 count= 46341 - position= 6 count= 8867 - position= 7 count= 8867 - position= 8 count= 3291 - position= 9 count= 3291 - position= 10 count= 3291 - position= 11 count= 3291 - position= 12 count= 3291 - position= 13 count= 35089 - position= 14 count= 35089 - position= 15 count= 35089 - position= 16 count= 35089 - position= 17 count= 35089 - position= 18 count= 35089 - position= 19 count= 35089 - position= 20 count= 30920 - position= 21 count= 30920 - position= 22 count= 30920 - position= 23 count= 17212 - position= 24 count= 17212 - position= 25 count= 39002 - position= 26 count= 39002 - position= 27 count= 39002 - position= 28 count= 39002 - position= 29 count= 49645 - position= 30 count= 49645 - position= 31 count= 49645 - position= 32 count= 49645 - position= 33 count= 49645 - position= 34 count= 49645 - position= 35 count= 49645 - position= 36 count= 49645 - position= 37 count= 49645 - position= 38 count= 49645 - position= 39 count= 10038 - position= 40 count= 10038 - position= 41 count= 10038 - position= 42 count= 10038 - position= 43 count= 10038 - position= 44 count= 10038 - position= 45 count= 10038 - position= 46 count= 10038 - position= 47 count= 10038 - position= 48 count= 10038 - position= 49 count= 32507 - position= 50 count= 32507 - position= 51 count= 32507 - position= 52 count= 32507 - position= 53 count= 24973 - position= 54 count= 24973 - position= 55 count= 24973 - position= 56 count= 24973 - position= 57 count= 24973 - position= 58 count= 24973 - position= 59 count= 24973 - position= 60 count= 24973 - position= 61 count= 49374 - position= 62 count= 49374 - position= 63 count= 49374 - position= 64 count= 49374 - position= 65 count= 49374 - position= 66 count= 49374 - position= 67 count= 49374 - position= 68 count= 49374 - position= 69 count= 45950 - position= 70 count= 45950 - position= 71 count= 45950 - position= 72 count= 45950 - position= 73 count= 45950 - position= 74 count= 45950 - position= 75 count= 45950 - position= 76 count= 45950 - position= 77 count= 45950 - position= 78 count= 45950 - position= 79 count= 14558 - position= 80 count= 14558 - position= 81 count= 14558 - position= 82 count= 14558 - position= 83 count= 14558 - position= 84 count= 14558 - position= 85 count= 17558 - position= 86 count= 17558 - position= 87 count= 17558 - position= 88 count= 17558 - position= 89 count= 17558 - position= 90 count= 17558 - position= 91 count= 17558 - position= 92 count= 17558 - position= 93 count= 17558 - position= 94 count= 17558 - position= 95 count= 42794 - position= 96 count= 42794 - position= 97 count= 42794 - position= 98 count= 42794 - position= 99 count= 25202 - position= 100 count= 25202 - position= 101 count= 25202 - position= 102 count= 10884 - position= 103 count= 10884 - position= 104 count= 10884 - position= 105 count= 10884 - position= 106 count= 10884 - position= 107 count= 10884 - position= 108 count= 34997 - position= 109 count= 34997 - position= 110 count= 34997 - position= 111 count= 39705 - position= 112 count= 39705 - position= 113 count= 39705 - position= 114 count= 39705 - position= 115 count= 39705 - position= 116 count= 39705 - position= 117 count= 39705 - position= 118 count= 39705 - position= 119 count= 39705 - position= 120 count= 39705 - position= 121 count= 16021 - position= 122 count= 16021 - position= 123 count= 27582 - position= 124 count= 27582 - position= 125 count= 27582 - position= 126 count= 27582 - position= 127 count= 27582 - position= 128 count= 27582 - position= 129 count= 27582 - position= 130 count= 27582 - position= 131 count= 27582 - position= 132 count= 4895 - position= 133 count= 4895 - position= 134 count= 4247 - position= 135 count= 6571 - position= 136 count= 37985 - position= 137 count= 37985 - position= 138 count= 37985 - position= 139 count= 37985 - position= 140 count= 37985 - position= 141 count= 37985 - position= 142 count= 36090 - position= 143 count= 36090 - position= 144 count= 36090 - position= 145 count= 36090 - position= 146 count= 36090 - position= 147 count= 12335 - position= 148 count= 12335 - position= 149 count= 12335 - position= 150 count= 12335 - position= 151 count= 12335 - position= 152 count= 12335 - position= 153 count= 12335 - position= 154 count= 12335 - position= 155 count= 41483 - position= 156 count= 41483 - position= 157 count= 41483 - position= 158 count= 41483 - position= 159 count= 41483 - position= 160 count= 41483 - position= 161 count= 41483 - position= 162 count= 42642 - position= 163 count= 42642 - position= 164 count= 42642 - position= 165 count= 42642 +Appending count: 285 length: 2 +Appending count: 36194 length: 10 +Appending count: 13261 length: 9 +Appending count: 44922 length: 9 +Appending count: 975 length: 8 +Appending count: 25753 length: 9 +Appending count: 25843 length: 6 +Appending count: 9163 length: 2 +Appending count: 46212 length: 6 +Appending count: 29600 length: 8 +Appending count: 7145 length: 2 +Appending count: 36315 length: 8 +Appending count: 3495 length: 6 +Appending count: 2445 length: 4 +Appending count: 18663 length: 5 +Appending count: 5352 length: 8 +Appending count: 10239 length: 5 +Appending count: 45891 length: 2 +Appending count: 43664 length: 5 +Appending count: 30745 length: 2 +Appending count: 33964 length: 2 +Appending count: 36478 length: 7 +Appending count: 3282 length: 6 +Appending count: 43616 length: 4 +Appending count: 11415 length: 2 +Appending count: 36997 length: 7 +Appending count: 19026 length: 2 +Appending count: 11655 length: 10 +Appending count: 26307 length: 1 +Appending count: 16185 length: 3 + position= 0 count= 285 + position= 1 count= 285 + position= 2 count= 36194 + position= 3 count= 36194 + position= 4 count= 36194 + position= 5 count= 36194 + position= 6 count= 36194 + position= 7 count= 36194 + position= 8 count= 36194 + position= 9 count= 36194 + position= 10 count= 36194 + position= 11 count= 36194 + position= 12 count= 13261 + position= 13 count= 13261 + position= 14 count= 13261 + position= 15 count= 13261 + position= 16 count= 13261 + position= 17 count= 13261 + position= 18 count= 13261 + position= 19 count= 13261 + position= 20 count= 13261 + position= 21 count= 44922 + position= 22 count= 44922 + position= 23 count= 44922 + position= 24 count= 44922 + position= 25 count= 44922 + position= 26 count= 44922 + position= 27 count= 44922 + position= 28 count= 44922 + position= 29 count= 44922 + position= 30 count= 975 + position= 31 count= 975 + position= 32 count= 975 + position= 33 count= 975 + position= 34 count= 975 + position= 35 count= 975 + position= 36 count= 975 + position= 37 count= 975 + position= 38 count= 25753 + position= 39 count= 25753 + position= 40 count= 25753 + position= 41 count= 25753 + position= 42 count= 25753 + position= 43 count= 25753 + position= 44 count= 25753 + position= 45 count= 25753 + position= 46 count= 25753 + position= 47 count= 25843 + position= 48 count= 25843 + position= 49 count= 25843 + position= 50 count= 25843 + position= 51 count= 25843 + position= 52 count= 25843 + position= 53 count= 9163 + position= 54 count= 9163 + position= 55 count= 46212 + position= 56 count= 46212 + position= 57 count= 46212 + position= 58 count= 46212 + position= 59 count= 46212 + position= 60 count= 46212 + position= 61 count= 29600 + position= 62 count= 29600 + position= 63 count= 29600 + position= 64 count= 29600 + position= 65 count= 29600 + position= 66 count= 29600 + position= 67 count= 29600 + position= 68 count= 29600 + position= 69 count= 7145 + position= 70 count= 7145 + position= 71 count= 36315 + position= 72 count= 36315 + position= 73 count= 36315 + position= 74 count= 36315 + position= 75 count= 36315 + position= 76 count= 36315 + position= 77 count= 36315 + position= 78 count= 36315 + position= 79 count= 3495 + position= 80 count= 3495 + position= 81 count= 3495 + position= 82 count= 3495 + position= 83 count= 3495 + position= 84 count= 3495 + position= 85 count= 2445 + position= 86 count= 2445 + position= 87 count= 2445 + position= 88 count= 2445 + position= 89 count= 18663 + position= 90 count= 18663 + position= 91 count= 18663 + position= 92 count= 18663 + position= 93 count= 18663 + position= 94 count= 5352 + position= 95 count= 5352 + position= 96 count= 5352 + position= 97 count= 5352 + position= 98 count= 5352 + position= 99 count= 5352 + position= 100 count= 5352 + position= 101 count= 5352 + position= 102 count= 10239 + position= 103 count= 10239 + position= 104 count= 10239 + position= 105 count= 10239 + position= 106 count= 10239 + position= 107 count= 45891 + position= 108 count= 45891 + position= 109 count= 43664 + position= 110 count= 43664 + position= 111 count= 43664 + position= 112 count= 43664 + position= 113 count= 43664 + position= 114 count= 30745 + position= 115 count= 30745 + position= 116 count= 33964 + position= 117 count= 33964 + position= 118 count= 36478 + position= 119 count= 36478 + position= 120 count= 36478 + position= 121 count= 36478 + position= 122 count= 36478 + position= 123 count= 36478 + position= 124 count= 36478 + position= 125 count= 3282 + position= 126 count= 3282 + position= 127 count= 3282 + position= 128 count= 3282 + position= 129 count= 3282 + position= 130 count= 3282 + position= 131 count= 43616 + position= 132 count= 43616 + position= 133 count= 43616 + position= 134 count= 43616 + position= 135 count= 11415 + position= 136 count= 11415 + position= 137 count= 36997 + position= 138 count= 36997 + position= 139 count= 36997 + position= 140 count= 36997 + position= 141 count= 36997 + position= 142 count= 36997 + position= 143 count= 36997 + position= 144 count= 19026 + position= 145 count= 19026 + position= 146 count= 11655 + position= 147 count= 11655 + position= 148 count= 11655 + position= 149 count= 11655 + position= 150 count= 11655 + position= 151 count= 11655 + position= 152 count= 11655 + position= 153 count= 11655 + position= 154 count= 11655 + position= 155 count= 11655 + position= 156 count= 26307 + position= 157 count= 16185 + position= 158 count= 16185 + position= 159 count= 16185 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) @@ -8177,7 +8207,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 4ms; used/avail/free/total/max mem: 122.74M/16.81G/103.75M/226.49M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 64.09M/16.79G/187.56M/251.66M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 @@ -8273,7 +8303,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 49.58M/16.88G/596.34M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 114.43M/16.74G/137.23M/251.66M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000 @@ -8288,7 +8318,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 141.86M/16.79G/504.06M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 64.36M/16.79G/187.30M/251.66M/16.85G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -8434,7 +8464,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 200.58M/16.73G/445.34M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 123.08M/16.73G/128.58M/251.66M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % found entry: query_index: 0 @@ -8482,7 +8512,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 229.94M/16.70G/415.98M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 151.05M/16.70G/100.61M/251.66M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000 @@ -8515,7 +8545,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 255.10M/16.67G/390.82M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 176.61M/16.68G/75.05M/251.66M/16.85G Second pass: writing the merged alignment. [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. @@ -8545,7 +8575,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 280.27M/16.65G/365.65M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 61.26M/16.79G/593.05M/654.31M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1 @@ -8636,10 +8666,10 @@ [main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 338.99M/16.59G/306.93M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 119.98M/16.73G/534.33M/654.31M/16.85G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -8789,7 +8819,7 @@ [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 10ms; used/avail/free/total/max mem: 53.72M/16.87G/592.20M/645.92M/16.93G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 212.25M/16.64G/442.06M/654.31M/16.85G [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 @@ -9186,7 +9216,7 @@ Annotations loaded Annotations loaded Annotations loaded -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 193.426 s - in TestSuite +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 115.33 s - in TestSuite [GobyRengine-ShutdownHook] INFO org.campagnelab.goby.R.GobyRengine - Shutdown hook is terminating R [INFO] [INFO] Results: @@ -9196,14 +9226,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.180 s] -[INFO] Goby I/O ........................................... SUCCESS [ 38.171 s] -[INFO] Goby Full Distribution ............................. SUCCESS [03:40 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.077 s] +[INFO] Goby I/O ........................................... SUCCESS [ 10.798 s] +[INFO] Goby Full Distribution ............................. SUCCESS [02:08 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 04:20 min -[INFO] Finished at: 2024-01-11T18:03:36-12:00 +[INFO] Total time: 02:19 min +[INFO] Finished at: 2025-02-14T02:32:23+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -9271,14 +9301,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 1.742 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.361 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.204 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.405 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.069 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.064 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 3.092 s -[INFO] Finished at: 2024-01-11T18:03:46-12:00 +[INFO] Total time: 0.708 s +[INFO] Finished at: 2025-02-14T02:32:25+14:00 [INFO] ------------------------------------------------------------------------  mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore Analysing pom.xml... @@ -9289,12 +9319,12 @@ > dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine -Jan 11, 2024 6:03:59 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Feb 14, 2025 2:32:31 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 -Jan 11, 2024 6:04:04 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Feb 14, 2025 2:32:37 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian @@ -9321,17 +9351,17 @@ dh_missing dh_installdeb dh_gencontrol +dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined -dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined -dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-9_all.deb'. dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-9_all.deb'. +dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-9_all.deb'. dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-9_amd64.buildinfo dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-9_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -9339,12 +9369,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2185384/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/3177718 and its subdirectories -I: Current time: Thu Jan 11 18:04:43 -12 2024 -I: pbuilder-time-stamp: 1705039483 +I: removing directory /srv/workspace/pbuilder/2185384 and its subdirectories +I: Current time: Fri Feb 14 02:32:46 +14 2025 +I: pbuilder-time-stamp: 1739449966