Diff of the two buildlogs: -- --- b1/build.log 2024-01-08 01:52:09.526159137 +0000 +++ b2/build.log 2024-01-08 01:58:14.789956916 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Jan 7 13:44:13 -12 2024 -I: pbuilder-time-stamp: 1704678253 +I: Current time: Sun Feb 9 22:15:12 +14 2025 +I: pbuilder-time-stamp: 1739088912 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/25149/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2550152/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +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 9 08:15 /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/2550152/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2550152/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='arm64' - DEBIAN_FRONTEND='noninteractive' + 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]="aarch64-unknown-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=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='bookworm' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=bookworm + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='59290ea922b74e17ae2ed0a7a9549856' - 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='25149' - PS1='# ' - PS2='> ' + INVOCATION_ID=33adf5962c2a4f4680a9eccf8d785332 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-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=2550152 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.U2dFG8wn/pbuilderrc_Y1sk --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.U2dFG8wn/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-9.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.104:3128' + 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.U2dFG8wn/pbuilderrc_b00L --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.U2dFG8wn/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-9.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.104:3128 I: uname -a - Linux codethink02-arm64 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-17-cloud-arm64 #1 SMP Debian 6.1.69-1 (2023-12-30) aarch64 GNU/Linux I: ls -l /bin total 7104 -rwxr-xr-x 1 root root 1346480 Apr 23 2023 bash @@ -143,15 +175,15 @@ -rwxr-xr-x 1 root root 68456 Sep 20 2022 readlink -rwxr-xr-x 1 root root 68592 Sep 20 2022 rm -rwxr-xr-x 1 root root 68480 Sep 20 2022 rmdir - -rwxr-xr-x 1 root root 68392 Jul 28 23:46 run-parts + -rwxr-xr-x 1 root root 68392 Jul 28 2023 run-parts -rwxr-xr-x 1 root root 134536 Jan 5 2023 sed - lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash + lrwxrwxrwx 1 root root 9 Feb 9 08:15 sh -> /bin/bash -rwxr-xr-x 1 root root 68432 Sep 20 2022 sleep -rwxr-xr-x 1 root root 134088 Sep 20 2022 stty -rwsr-xr-x 1 root root 133312 Mar 23 2023 su -rwxr-xr-x 1 root root 68448 Sep 20 2022 sync -rwxr-xr-x 1 root root 539896 Apr 6 2023 tar - -rwxr-xr-x 1 root root 67904 Jul 28 23:46 tempfile + -rwxr-xr-x 1 root root 67904 Jul 28 2023 tempfile -rwxr-xr-x 1 root root 134160 Sep 20 2022 touch -rwxr-xr-x 1 root root 68384 Sep 20 2022 true -rwxr-xr-x 1 root root 67664 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/25149/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2550152/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -715,7 +747,7 @@ Get: 426 http://deb.debian.org/debian bookworm/main arm64 r-base-core arm64 4.2.2.20221110-2 [25.7 MB] Get: 427 http://deb.debian.org/debian bookworm/main arm64 r-cran-rjava arm64 1.0-6-1+b1 [916 kB] Get: 428 http://deb.debian.org/debian bookworm/main arm64 testng all 6.9.12-4 [795 kB] -Fetched 371 MB in 5s (73.7 MB/s) +Fetched 371 MB in 2s (213 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 18171 files and directories currently installed.) @@ -2090,8 +2122,8 @@ Setting up tzdata (2023c-5+deb12u1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jan 8 01:46:27 UTC 2024. -Universal Time is now: Mon Jan 8 01:46:27 UTC 2024. +Local time is now: Sun Feb 9 08:16:04 UTC 2025. +Universal Time is now: Sun Feb 9 08:16:04 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2646,7 +2678,11 @@ 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/2550152/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for bookworm +I: user script /srv/workspace/pbuilder/2550152/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 @@ -6193,14 +6229,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.064 s] -[INFO] Goby I/O ........................................... SUCCESS [ 31.590 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 47.245 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.060 s] +[INFO] Goby I/O ........................................... SUCCESS [ 22.521 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 23.512 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:19 min -[INFO] Finished at: 2024-01-07T13:48:07-12:00 +[INFO] Total time: 46.239 s +[INFO] Finished at: 2025-02-09T22:17:20+14:00 [INFO] ------------------------------------------------------------------------  debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -6497,46 +6533,46 @@ [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 47913.5 for sample B-7 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47913.5 for sample B-3 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98572.5 for sample A-3 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98703.2 for sample A-12 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48828.7 for sample B-15 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47717.4 for sample B-14 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50920.4 for sample B-11 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 101449 for sample A-17 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49743.8 for sample B-2 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49351.6 for sample B-10 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98311.0 for sample A-16 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48894.0 for sample B-8 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47717.4 for sample B-4 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99160.8 for sample A-2 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99879.8 for sample A-0 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49286.2 for sample B-6 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98114.9 for sample A-9 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 96088.6 for sample A-8 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98376.4 for sample A-5 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98114.9 for sample A-4 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 96938.3 for sample A-6 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98899.3 for sample A-7 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48501.8 for sample B-5 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98376.4 for sample A-10 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97984.2 for sample A-14 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47129.2 for sample B-9 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98376.4 for sample A-1 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48371.1 for sample B-0 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49024.8 for sample B-12 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48567.2 for sample B-13 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99030.0 for sample A-19 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 96873.0 for sample A-18 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 95042.7 for sample A-15 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48959.4 for sample B-1 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97199.8 for sample A-13 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99814.4 for sample A-11 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47129.2 for sample B-16 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49090.1 for sample B-17 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48632.6 for sample B-19 -[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48828.7 for sample B-18 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 57418.6 for sample B-7 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 54431.9 for sample B-3 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 112373 for sample A-3 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 111851 for sample A-12 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55850.6 for sample B-15 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 54207.9 for sample B-14 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56149.3 for sample B-11 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 110656 for sample A-17 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55775.9 for sample B-2 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55253.3 for sample B-10 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 113344 for sample A-16 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 57194.6 for sample B-8 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56746.6 for sample B-4 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 113419 for sample A-2 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 114912 for sample A-0 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56671.9 for sample B-6 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 111925 for sample A-9 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 112149 for sample A-8 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 111627 for sample A-5 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 111253 for sample A-4 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 106475 for sample A-6 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 110283 for sample A-7 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55775.9 for sample B-5 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 106475 for sample A-10 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 109685 for sample A-14 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55925.3 for sample B-9 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 113269 for sample A-1 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56223.9 for sample B-0 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56223.9 for sample B-12 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56522.6 for sample B-13 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 113419 for sample A-19 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 107520 for sample A-18 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 112373 for sample A-15 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 54954.6 for sample B-1 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 110432 for sample A-13 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 112224 for sample A-11 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 55925.3 for sample B-16 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 53610.6 for sample B-17 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56447.9 for sample B-19 +[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 56223.9 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. @@ -6601,7 +6637,7 @@ [ 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 [0.9947776393635362, 0.4985218718045486, -0.007554015903009714, -1.0042712930688047, 0.0, 0.0] ] +[ id-1 [1.0027194574810867, 0.4989545497187827, 0.003918022785035809, -1.0030196899093726, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 @@ -7519,208 +7555,207 @@ Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 -Appending count: 25209 length: 1 -Appending count: 18735 length: 2 -Appending count: 4261 length: 10 -Appending count: 24674 length: 8 -Appending count: 42727 length: 9 -Appending count: 14245 length: 2 -Appending count: 11310 length: 2 -Appending count: 17363 length: 10 -Appending count: 1305 length: 4 -Appending count: 46558 length: 10 -Appending count: 27777 length: 2 -Appending count: 40605 length: 6 -Appending count: 8131 length: 8 -Appending count: 7553 length: 6 -Appending count: 26680 length: 8 -Appending count: 28466 length: 3 -Appending count: 6131 length: 6 -Appending count: 4554 length: 2 -Appending count: 36855 length: 10 -Appending count: 42894 length: 4 -Appending count: 40546 length: 9 -Appending count: 28309 length: 6 -Appending count: 29210 length: 3 -Appending count: 13686 length: 7 -Appending count: 3923 length: 8 -Appending count: 44818 length: 3 -Appending count: 1290 length: 6 -Appending count: 6699 length: 4 -Appending count: 4929 length: 3 -Appending count: 6784 length: 10 - position= 0 count= 25209 - position= 1 count= 18735 - position= 2 count= 18735 - position= 3 count= 4261 - position= 4 count= 4261 - position= 5 count= 4261 - position= 6 count= 4261 - position= 7 count= 4261 - position= 8 count= 4261 - position= 9 count= 4261 - position= 10 count= 4261 - position= 11 count= 4261 - position= 12 count= 4261 - position= 13 count= 24674 - position= 14 count= 24674 - position= 15 count= 24674 - position= 16 count= 24674 - position= 17 count= 24674 - position= 18 count= 24674 - position= 19 count= 24674 - position= 20 count= 24674 - position= 21 count= 42727 - position= 22 count= 42727 - position= 23 count= 42727 - position= 24 count= 42727 - position= 25 count= 42727 - position= 26 count= 42727 - position= 27 count= 42727 - position= 28 count= 42727 - position= 29 count= 42727 - position= 30 count= 14245 - position= 31 count= 14245 - position= 32 count= 11310 - position= 33 count= 11310 - position= 34 count= 17363 - position= 35 count= 17363 - position= 36 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position= 6 count= 40936 + position= 7 count= 40936 + position= 8 count= 40936 + position= 9 count= 40936 + position= 10 count= 40936 + position= 11 count= 31977 + position= 12 count= 31977 + position= 13 count= 31977 + position= 14 count= 41069 + position= 15 count= 41069 + position= 16 count= 41069 + position= 17 count= 41069 + position= 18 count= 41069 + position= 19 count= 23602 + position= 20 count= 23602 + position= 21 count= 23602 + position= 22 count= 23602 + position= 23 count= 23602 + position= 24 count= 23602 + position= 25 count= 23602 + position= 26 count= 30021 + position= 27 count= 30021 + position= 28 count= 30021 + position= 29 count= 30021 + position= 30 count= 30021 + position= 31 count= 30021 + position= 32 count= 30021 + position= 33 count= 30021 + position= 34 count= 32282 + position= 35 count= 32282 + position= 36 count= 32282 + position= 37 count= 5495 + position= 38 count= 5495 + position= 39 count= 5495 + position= 40 count= 5495 + position= 41 count= 5495 + position= 42 count= 5495 + position= 43 count= 5495 + position= 44 count= 5495 + position= 45 count= 5495 + position= 46 count= 5495 + position= 47 count= 48304 + position= 48 count= 45154 + position= 49 count= 45154 + position= 50 count= 45154 + position= 51 count= 45154 + position= 52 count= 45154 + position= 53 count= 45154 + position= 54 count= 45154 + position= 55 count= 47170 + position= 56 count= 22036 + position= 57 count= 22036 + position= 58 count= 22036 + position= 59 count= 27936 + position= 60 count= 27936 + position= 61 count= 27936 + position= 62 count= 27936 + position= 63 count= 27936 + position= 64 count= 27936 + position= 65 count= 27936 + position= 66 count= 27936 + position= 67 count= 26936 + position= 68 count= 26936 + position= 69 count= 26936 + position= 70 count= 26936 + position= 71 count= 26936 + position= 72 count= 26936 + position= 73 count= 26936 + position= 74 count= 26936 + position= 75 count= 26936 + position= 76 count= 9167 + position= 77 count= 9167 + position= 78 count= 9167 + position= 79 count= 9167 + position= 80 count= 9167 + position= 81 count= 9167 + position= 82 count= 30716 + position= 83 count= 30716 + position= 84 count= 30716 + position= 85 count= 30716 + position= 86 count= 30716 + position= 87 count= 32873 + position= 88 count= 32873 + position= 89 count= 32873 + position= 90 count= 32873 + position= 91 count= 30096 + position= 92 count= 30096 + position= 93 count= 30096 + position= 94 count= 30096 + position= 95 count= 30096 + position= 96 count= 30096 + position= 97 count= 30096 + position= 98 count= 30096 + position= 99 count= 30096 + position= 100 count= 16657 + position= 101 count= 16657 + position= 102 count= 16657 + position= 103 count= 11051 + position= 104 count= 11051 + position= 105 count= 29508 + position= 106 count= 29508 + position= 107 count= 29508 + position= 108 count= 29508 + position= 109 count= 29508 + position= 110 count= 29508 + position= 111 count= 29508 + position= 112 count= 29508 + position= 113 count= 29508 + position= 114 count= 29508 + position= 115 count= 40199 + position= 116 count= 40199 + position= 117 count= 40199 + position= 118 count= 40199 + position= 119 count= 40199 + position= 120 count= 40199 + position= 121 count= 19227 + position= 122 count= 19227 + position= 123 count= 19227 + position= 124 count= 19227 + position= 125 count= 19227 + position= 126 count= 32940 + position= 127 count= 32940 + position= 128 count= 32940 + position= 129 count= 32940 + position= 130 count= 32940 + position= 131 count= 32940 + position= 132 count= 32940 + position= 133 count= 45453 + position= 134 count= 45453 + position= 135 count= 45453 + position= 136 count= 45453 + position= 137 count= 45453 + position= 138 count= 45453 + position= 139 count= 45453 + position= 140 count= 45453 + position= 141 count= 45453 + position= 142 count= 37899 + position= 143 count= 37899 + position= 144 count= 37899 + position= 145 count= 37899 + position= 146 count= 37899 + position= 147 count= 48930 + position= 148 count= 48930 + position= 149 count= 48930 + position= 150 count= 48930 + position= 151 count= 48930 + position= 152 count= 48930 + position= 153 count= 48930 + position= 154 count= 41648 + position= 155 count= 41648 + position= 156 count= 26354 + position= 157 count= 26354 + position= 158 count= 26354 + position= 159 count= 26354 + position= 160 count= 26354 + position= 161 count= 26354 + position= 162 count= 26354 + position= 163 count= 26354 + position= 164 count= 26354 + position= 165 count= 26354 + position= 166 count= 37419 + position= 167 count= 37419 + position= 168 count= 37419 + position= 169 count= 37419 + position= 170 count= 37419 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) @@ -8173,7 +8208,7 @@ [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: 2ms; used/avail/free/total/max mem: 44.27M/8.36G/165.44M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 6ms; used/avail/free/total/max mem: 114.83M/8.29G/69.72M/184.55M/8.40G [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 @@ -8269,7 +8304,7 @@ [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: 88.33M/8.31G/121.38M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 62.91M/8.34G/121.64M/184.55M/8.40G [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 @@ -8284,7 +8319,7 @@ [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: 67.66M/8.33G/142.06M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 48.26M/8.35G/136.29M/184.55M/8.40G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -8430,7 +8465,7 @@ [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: 126.39M/8.27G/83.32M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 109.06M/8.29G/75.49M/184.55M/8.40G [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 @@ -8478,7 +8513,7 @@ [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: 153.64M/8.25G/56.08M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 134.22M/8.27G/50.32M/184.55M/8.40G [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 @@ -8511,7 +8546,7 @@ [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: 60.96M/8.34G/148.76M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 56.32M/8.34G/128.23M/184.55M/8.40G 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. @@ -8541,7 +8576,7 @@ [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: 86.13M/8.32G/123.59M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 81.47M/8.32G/103.08M/184.55M/8.40G [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 @@ -8635,7 +8670,7 @@ [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: 144.85M/8.26G/64.87M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 35.68M/8.37G/333.42M/369.10M/8.40G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -8785,7 +8820,7 @@ [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: 2ms; used/avail/free/total/max mem: 115.72M/8.29G/94.00M/209.72M/8.40G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 127.91M/8.27G/241.19M/369.10M/8.40G [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 @@ -9182,7 +9217,7 @@ Annotations loaded Annotations loaded Annotations loaded -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 155.288 s - in TestSuite +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 152.088 s - in TestSuite [GobyRengine-ShutdownHook] INFO org.campagnelab.goby.R.GobyRengine - Shutdown hook is terminating R [INFO] [INFO] Results: @@ -9192,14 +9227,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.099 s] -[INFO] Goby I/O ........................................... SUCCESS [ 16.487 s] -[INFO] Goby Full Distribution ............................. SUCCESS [02:51 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.070 s] +[INFO] Goby I/O ........................................... SUCCESS [ 8.489 s] +[INFO] Goby Full Distribution ............................. SUCCESS [02:48 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 03:08 min -[INFO] Finished at: 2024-01-07T13:51:19-12:00 +[INFO] Total time: 02:58 min +[INFO] Finished at: 2025-02-09T22:20:20+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -9267,14 +9302,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.899 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.276 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.145 s] +[INFO] Goby Framework ..................................... SUCCESS [ 1.516 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.379 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.380 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 1.703 s -[INFO] Finished at: 2024-01-07T13:51:24-12:00 +[INFO] Total time: 2.945 s +[INFO] Finished at: 2025-02-09T22:20:37+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... @@ -9285,12 +9320,12 @@ > 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 07, 2024 1:51:34 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Feb 09, 2025 10:20:49 PM org.debian.maven.packager.DependenciesSolver$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 07, 2024 1:51:40 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Feb 09, 2025 10:20:55 PM org.debian.maven.packager.DependenciesSolver$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 @@ -9317,11 +9352,11 @@ 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 dh_md5sums @@ -9335,12 +9370,14 @@ 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/2550152/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2550152/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/25149 and its subdirectories -I: Current time: Sun Jan 7 13:52:08 -12 2024 -I: pbuilder-time-stamp: 1704678728 +I: removing directory /srv/workspace/pbuilder/2550152 and its subdirectories +I: Current time: Sun Feb 9 22:21:13 +14 2025 +I: pbuilder-time-stamp: 1739089273