Diff of the two buildlogs:
--
--- b1/build.log 2023-04-16 14:27:02.519777012 +0000
+++ b2/build.log 2023-04-16 14:29:00.466545702 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Sun Apr 16 02:24:42 -12 2023
-I: pbuilder-time-stamp: 1681655082
+I: Current time: Sun May 19 10:50:04 +14 2024
+I: pbuilder-time-stamp: 1716065404
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
@@ -16,7 +16,7 @@
I: copying [./artfastqgenerator_0.0.20150519.orig.tar.xz]
I: copying [./artfastqgenerator_0.0.20150519-4.debian.tar.xz]
I: Extracting source
-gpgv: Signature made Mon Nov 16 02:29:10 2020 -12
+gpgv: Signature made Tue Nov 17 04:29:10 2020 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
@@ -28,52 +28,84 @@
dpkg-source: info: applying adapt_doc.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/26553/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/17450/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink11-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 May 19 10:50 /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/17450/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/17450/tmp/hooks/D02_print_environment starting
I: set
- BUILDDIR='/build'
- 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
+ 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=8'
- DISTRIBUTION='bookworm'
- HOME='/var/lib/jenkins'
- HOST_ARCH='arm64'
+ DIRSTACK=()
+ DISTRIBUTION=bookworm
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/var/lib/jenkins
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=aarch64
+ HOST_ARCH=arm64
IFS='
'
- 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='26553'
- PS1='# '
- PS2='> '
+ 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=17450
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.Kl1NZn3T/pbuilderrc_Z43h --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.Kl1NZn3T/b1 --logfile b1/build.log artfastqgenerator_0.0.20150519-4.dsc'
- SUDO_GID='117'
- SUDO_UID='110'
- SUDO_USER='jenkins'
- TERM='unknown'
- TZ='/usr/share/zoneinfo/Etc/GMT+12'
- USER='root'
- USERNAME='root'
- _='/usr/bin/systemd-run'
- http_proxy='http://192.168.101.16:3128'
+ 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.Kl1NZn3T/pbuilderrc_KPRv --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.Kl1NZn3T/b2 --logfile b2/build.log --extrapackages usrmerge artfastqgenerator_0.0.20150519-4.dsc'
+ SUDO_GID=117
+ SUDO_UID=110
+ SUDO_USER=jenkins
+ TERM=unknown
+ TZ=/usr/share/zoneinfo/Etc/GMT-14
+ UID=0
+ USER=root
+ USERNAME=root
+ _='I: set'
+ http_proxy=http://192.168.101.16:3128
I: uname -a
- Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux
+ Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Apr 15 22:25 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/26553/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 May 19 06:48 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/17450/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -321,7 +353,7 @@
Get: 206 http://deb.debian.org/debian bookworm/main arm64 wdiff arm64 1.2.2-5 [119 kB]
Get: 207 http://deb.debian.org/debian bookworm/main arm64 devscripts arm64 2.23.3 [1073 kB]
Get: 208 http://deb.debian.org/debian bookworm/main arm64 javahelper all 0.78 [97.2 kB]
-Fetched 362 MB in 28s (12.8 MB/s)
+Fetched 362 MB in 32s (11.4 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%
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(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 ... 19616 files and directories currently installed.)
@@ -1353,8 +1385,17 @@
Writing extended state information...
Building tag database...
-> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+usrmerge is already the newest version (35).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Building the package
-I: Running cd /build/artfastqgenerator-0.0.20150519/ && 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 > ../artfastqgenerator_0.0.20150519-4_source.changes
+I: user script /srv/workspace/pbuilder/17450/tmp/hooks/A99_set_merged_usr starting
+Re-configuring usrmerge...
+I: user script /srv/workspace/pbuilder/17450/tmp/hooks/A99_set_merged_usr finished
+hostname: Temporary failure in name resolution
+I: Running cd /build/artfastqgenerator-0.0.20150519/ && 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 > ../artfastqgenerator_0.0.20150519-4_source.changes
dpkg-buildpackage: info: source package artfastqgenerator
dpkg-buildpackage: info: source version 0.0.20150519-4
dpkg-buildpackage: info: source distribution unstable
@@ -1393,66 +1434,66 @@
You should have received a copy of the GNU General Public License along with this program; if not, see <http://www.gnu.org/licenses>.
-Apr 16, 2023 2:26:41 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
+May 19, 2024 10:51:44 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
INFO: Found the start sequence ID str >1 in >1 dna:chromosome chromosome:GRCh37:1:1:249250621:1
-Apr 16, 2023 2:26:41 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
+May 19, 2024 10:51:44 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
INFO: Read generation begun.
-Apr 16, 2023 2:26:41 AM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader
+May 19, 2024 10:51:44 AM artificialFastqGenerator.CoverageStatisticsCalculator logCoverageStatsHeader
INFO: ALL_SO_FAR_NUM,ALL_AV_COV,ALL_MIN_COV,ALL_MAX_COV,ACGT_NUM,ACGT_AV_COV,ACGT_MIN_COV,ACGT_MAX_COV
-Apr 16, 2023 2:26:42 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 10000,27.1137,1,51,9880,27.362955465587046,5,51
-Apr 16, 2023 2:26:42 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 20000,29.8134,6,49,10000,29.8134,6,49
-Apr 16, 2023 2:26:43 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 30000,33.8232,11,56,10000,33.8232,11,56
-Apr 16, 2023 2:26:43 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 40000,30.4908,7,46,10000,30.4908,7,46
-Apr 16, 2023 2:26:43 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 50000,32.5411,12,49,10000,32.5411,12,49
-Apr 16, 2023 2:26:44 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 60000,28.5939,3,49,10000,28.5939,3,49
-Apr 16, 2023 2:26:44 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 70000,31.8053,13,58,10000,31.8053,13,58
-Apr 16, 2023 2:26:44 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 80000,29.961,11,50,10000,29.961,11,50
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 90000,32.6258,13,57,10000,32.6258,13,57
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
+May 19, 2024 10:51:44 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 10000,28.6318,1,53,9880,28.856578947368423,3,53
+May 19, 2024 10:51:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 20000,30.0908,4,52,10000,30.0908,4,52
+May 19, 2024 10:51:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 30000,32.6849,13,55,10000,32.6849,13,55
+May 19, 2024 10:51:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 40000,30.2559,11,49,10000,30.2559,11,49
+May 19, 2024 10:51:46 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 50000,31.8629,10,56,10000,31.8629,10,56
+May 19, 2024 10:51:46 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 60000,30.0764,2,52,10000,30.0764,2,52
+May 19, 2024 10:51:46 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 70000,31.0245,11,53,10000,31.0245,11,53
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 80000,29.4067,10,51,10000,29.4067,10,51
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 90000,34.6967,13,59,10000,34.6967,13,59
+May 19, 2024 10:51:47 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
INFO: Found the end sequence identifier > in >2 dna:chromosome chromosome:GRCh37:2:1:243199373:1
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
+May 19, 2024 10:51:47 AM artificialFastqGenerator.ArtificialFastqGenerator generateArtificialFastqs
INFO: Further reads generated only for nucleobases already in memory.
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 100000,32.79,4,53,9960,32.888253012048196,4,53
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
-INFO: 100080,4.425,0,9,0,0.0,0,0
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 100000,34.1621,5,54,9960,34.26897590361446,5,54
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logRegionStats
+INFO: 100080,3.7125,0,6,0,0.0,0,0
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
INFO:
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
INFO: OVERALL STATISTICS:
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
INFO: # nucleobases processed=100080
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
-INFO: Average coverage=30.934612310151877
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+INFO: Average coverage=31.26722621902478
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
INFO: Minimum coverage=0
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
-INFO: Maximum coverage=58
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+INFO: Maximum coverage=59
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
INFO: # ACGTs processed=99840
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
-INFO: ACGT average coverage=30.994170673076923
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
-INFO: ACGT minimum coverage=3
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
-INFO: ACGT maximum coverage=58
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
-INFO: # reads=40736
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
-INFO: # nucleobase calls=3095936
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
-INFO: # ACGT nucleobase calls=3094458
-Apr 16, 2023 2:26:45 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
-INFO: # ACGT call errors=178877
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+INFO: ACGT average coverage=31.32421875
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+INFO: ACGT minimum coverage=2
+May 19, 2024 10:51:47 AM artificialFastqGenerator.CoverageStatisticsCalculator logOverallStats
+INFO: ACGT maximum coverage=59
+May 19, 2024 10:51:47 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
+INFO: # reads=41174
+May 19, 2024 10:51:47 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
+INFO: # nucleobase calls=3129224
+May 19, 2024 10:51:47 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
+INFO: # ACGT nucleobase calls=3127410
+May 19, 2024 10:51:47 AM artificialFastqGenerator.NucleobaseAndReadFactory logOverallErrorStats
+INFO: # ACGT call errors=182945
rm C1.1.fastq C1.2.fastq
make[1]: Leaving directory '/build/artfastqgenerator-0.0.20150519'
create-stamp debian/debhelper-build-stamp
@@ -1478,8 +1519,8 @@
dh_md5sums
dh_builddeb
dpkg-deb: building package 'artfastqgenerator' in '../artfastqgenerator_0.0.20150519-4_all.deb'.
-dpkg-deb: building package 'artfastqgenerator-examples' in '../artfastqgenerator-examples_0.0.20150519-4_all.deb'.
dpkg-deb: building package 'artfastqgenerator-doc' in '../artfastqgenerator-doc_0.0.20150519-4_all.deb'.
+dpkg-deb: building package 'artfastqgenerator-examples' in '../artfastqgenerator-examples_0.0.20150519-4_all.deb'.
dpkg-genbuildinfo --build=binary -O../artfastqgenerator_0.0.20150519-4_arm64.buildinfo
dpkg-genchanges --build=binary -O../artfastqgenerator_0.0.20150519-4_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1487,12 +1528,14 @@
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/17450/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/17450/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/26553 and its subdirectories
-I: Current time: Sun Apr 16 02:27:01 -12 2023
-I: pbuilder-time-stamp: 1681655221
+I: removing directory /srv/workspace/pbuilder/17450 and its subdirectories
+I: Current time: Sun May 19 10:51:58 +14 2024
+I: pbuilder-time-stamp: 1716065518