Diff of the two buildlogs:
--
--- b1/build.log 2025-02-17 19:02:37.912476807 +0000
+++ b2/build.log 2025-02-17 19:08:45.940002147 +0000
@@ -1,6 +1,6 @@
I: pbuilder: network access will be disabled during build
-I: Current time: Mon Feb 17 06:48:00 -12 2025
-I: pbuilder-time-stamp: 1739818080
+I: Current time: Mon Mar 23 15:25:41 +14 2026
+I: pbuilder-time-stamp: 1774229141
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
@@ -27,52 +27,84 @@
dpkg-source: info: applying test_scope_for_junit.patch
I: Not using root during the build.
I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/1865035/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/557284/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink03-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 Mar 23 01:25 /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/557284/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/557284/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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+ BASH_VERSION='5.2.37(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='unstable'
- HOME='/root'
- HOST_ARCH='arm64'
+ DIRSTACK=()
+ DISTRIBUTION=unstable
+ EUID=0
+ FUNCNAME=([0]="Echo" [1]="main")
+ GROUPS=()
+ HOME=/root
+ HOSTNAME=i-capture-the-hostname
+ HOSTTYPE=aarch64
+ HOST_ARCH=arm64
IFS='
'
- INVOCATION_ID='949f5bfd5a6e4f9492650b7d691ff32e'
- 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='1865035'
- PS1='# '
- PS2='> '
+ INVOCATION_ID=326e5bd9dd0145efb7c1ca5cdcfd9b5c
+ 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=557284
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.coq3NiGe/pbuilderrc_X1iy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.coq3NiGe/b1 --logfile b1/build.log snpsift_5.2.e+dfsg-2.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://192.168.101.4:3128'
+ 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.coq3NiGe/pbuilderrc_EOeF --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.coq3NiGe/b2 --logfile b2/build.log snpsift_5.2.e+dfsg-2.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://192.168.101.4:3128
I: uname -a
- Linux codethink04-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
+ Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
I: ls -l /bin
- lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/1865035/tmp/hooks/D02_print_environment finished
+ lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/557284/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
@@ -461,7 +493,7 @@
Get: 321 http://deb.debian.org/debian unstable/main arm64 maven-repo-helper all 1.11 [142 kB]
Get: 322 http://deb.debian.org/debian unstable/main arm64 unzip arm64 6.0-28+b1 [158 kB]
Get: 323 http://deb.debian.org/debian unstable/main arm64 maven-debian-helper all 2.6.7 [108 kB]
-Fetched 311 MB in 4s (83.4 MB/s)
+Fetched 311 MB in 1s (232 MB/s)
Preconfiguring packages ...
Selecting previously unselected package libpipeline1: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 ... 19918 files and directories currently installed.)
@@ -1511,8 +1543,8 @@
Setting up tzdata (2025a-2) ...
Current default time zone: 'Etc/UTC'
-Local time is now: Mon Feb 17 18:49:56 UTC 2025.
-Universal Time is now: Mon Feb 17 18:49:56 UTC 2025.
+Local time is now: Mon Mar 23 01:26:31 UTC 2026.
+Universal Time is now: Mon Mar 23 01:26:31 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ...
@@ -1978,7 +2010,11 @@
Building tag database...
-> Finished parsing the build-deps
I: Building the package
-I: Running cd /build/reproducible-path/snpsift-5.2.e+dfsg/ && 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 > ../snpsift_5.2.e+dfsg-2_source.changes
+I: user script /srv/workspace/pbuilder/557284/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/557284/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/snpsift-5.2.e+dfsg/ && 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 > ../snpsift_5.2.e+dfsg-2_source.changes
dpkg-buildpackage: info: source package snpsift
dpkg-buildpackage: info: source version 5.2.e+dfsg-2
dpkg-buildpackage: info: source distribution unstable
@@ -1991,7 +2027,7 @@
bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
mh_unpatchpoms -plibsnpsift-java
jh_clean
-Duplicate specification "u=s" for option "u"
+Duplicate specification "unlink|u" for option "u"
debian/rules override_dh_clean
make[1]: Entering directory '/build/reproducible-path/snpsift-5.2.e+dfsg'
# Removing all the sidx files created during the tests. Then one of them must
@@ -2403,8 +2439,8 @@
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 46.389 s
-[INFO] Finished at: 2025-02-17T06:53:13-12:00
+[INFO] Total time: 17.224 s
+[INFO] Finished at: 2026-03-23T15:27:23+14:00
[INFO] ------------------------------------------------------------------------
debian/rules execute_before_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/snpsift-5.2.e+dfsg'
@@ -2486,7 +2522,7 @@
TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test
TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test
TestCasesAnnotate.test_27_repeat_db_entry(580): Test
-[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.822 s - in org.snpsift.tests.unit.TestCasesAnnotateTabix
+[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 24.791 s - in org.snpsift.tests.unit.TestCasesAnnotateTabix
[INFO] Running org.snpsift.tests.unit.TestCasesEnumArray
EnumArray: length: 17 / 17, number of enums: 6
0: 'one' (1)
@@ -2500,13 +2536,13 @@
8: 'three' (3)
9: 'four' (4)
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.933 s - in org.snpsift.tests.unit.TestCasesEnumArray
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.649 s - in org.snpsift.tests.unit.TestCasesEnumArray
[INFO] Running org.snpsift.tests.unit.TestCasesIntervals
TestCasesIntervals.test_01(25): Test
TestCasesIntervals.test_02(50): Test
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesIntervals
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.snpsift.tests.unit.TestCasesIntervals
[INFO] Running org.snpsift.tests.unit.TestCasesFilterChrPos
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 s - in org.snpsift.tests.unit.TestCasesFilterChrPos
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.034 s - in org.snpsift.tests.unit.TestCasesFilterChrPos
[INFO] Running org.snpsift.tests.unit.TestCasesAnnotateUseIndex
TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test
TestCasesAnnotate.test_29_repeated_IDs(618): Test
@@ -2550,7 +2586,7 @@
TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test
TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test
TestCasesAnnotate.test_27_repeat_db_entry(580): Test
-[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 33.17 s - in org.snpsift.tests.unit.TestCasesAnnotateUseIndex
+[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.023 s - in org.snpsift.tests.unit.TestCasesAnnotateUseIndex
[INFO] Running org.snpsift.tests.unit.TestCasesAnnotateMem
TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test
TestCasesAnnotate.test_29_repeated_IDs(618): Test
@@ -2594,11 +2630,11 @@
TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test
TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test
TestCasesAnnotate.test_27_repeat_db_entry(580): Test
-[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 42.519 s - in org.snpsift.tests.unit.TestCasesAnnotateMem
+[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.465 s - in org.snpsift.tests.unit.TestCasesAnnotateMem
[INFO] Running org.snpsift.tests.unit.TestCasesFilterGt
TestCasesFilterGt.test_01(28): Test
TestCasesFilterGt.test_02(62): Test
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.271 s - in org.snpsift.tests.unit.TestCasesFilterGt
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.062 s - in org.snpsift.tests.unit.TestCasesFilterGt
[INFO] Running org.snpsift.tests.unit.TestCasesConcordance
TestCasesConcordance.test_01(68): Test
TestCasesConcordance.test_02(74): Test
@@ -2612,9 +2648,9 @@
TestCasesConcordance.test_10(153): Test
TestCasesConcordance.test_11(164): Test
TestCasesConcordance.test_12(181): Test
-[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.257 s - in org.snpsift.tests.unit.TestCasesConcordance
+[INFO] Tests run: 12, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.057 s - in org.snpsift.tests.unit.TestCasesConcordance
[INFO] Running org.snpsift.tests.unit.TestCasesVariantTypeCounter
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.049 s - in org.snpsift.tests.unit.TestCasesVariantTypeCounter
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesVariantTypeCounter
[INFO] Running org.snpsift.tests.unit.TestCasesAnnotateCreateIndex
TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test
TestCasesAnnotate.test_29_repeated_IDs(618): Test
@@ -2658,9 +2694,9 @@
TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test
TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test
TestCasesAnnotate.test_27_repeat_db_entry(580): Test
-[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 42.919 s - in org.snpsift.tests.unit.TestCasesAnnotateCreateIndex
+[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 23.122 s - in org.snpsift.tests.unit.TestCasesAnnotateCreateIndex
[INFO] Running org.snpsift.tests.unit.TestCasesStringArray
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 70.565 s - in org.snpsift.tests.unit.TestCasesStringArray
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 19.881 s - in org.snpsift.tests.unit.TestCasesStringArray
[INFO] Running org.snpsift.tests.unit.TestCasesCaseControl
TestCasesCaseControl.test_01(53): Test
TestCasesCaseControl.test_02(65): Test
@@ -2679,13 +2715,13 @@
TestCasesCaseControl.test_02_Str(71): Test
TestCasesCaseControl.test_03_Str(89): Test
TestCasesCaseControl.test_04_Str(113): Test
-[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.186 s - in org.snpsift.tests.unit.TestCasesCaseControl
+[INFO] Tests run: 17, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.225 s - in org.snpsift.tests.unit.TestCasesCaseControl
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnBool
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.334 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnBool
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.928 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnBool
[INFO] Running org.snpsift.tests.unit.TestCasesIndex
TestCasesIndex.test_01(32): Test
TestCasesIndex.test_02(84): Test
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 6.134 s - in org.snpsift.tests.unit.TestCasesIndex
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.627 s - in org.snpsift.tests.unit.TestCasesIndex
[INFO] Running org.snpsift.tests.unit.TestCasesPrivate
TestCasesPrivate.test_01(48): Test
TestCasesPrivate.test_02(59): Test
@@ -2695,19 +2731,19 @@
TestCasesPrivate.test_06(95): Test
TestCasesPrivate.test_07(101): Test
TestCasesPrivate.test_08(107): Test
-[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.021 s - in org.snpsift.tests.unit.TestCasesPrivate
+[INFO] Tests run: 8, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.005 s - in org.snpsift.tests.unit.TestCasesPrivate
[INFO] Running org.snpsift.tests.unit.TestCasesSplit
TestCasesSplit.test_01(28): Test
TestCasesSplit.test_02(58): Test
TestCasesSplit.test_03(84): Test
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.016 s - in org.snpsift.tests.unit.TestCasesSplit
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.tests.unit.TestCasesSplit
[INFO] Running org.snpsift.tests.unit.TestCasesVarType
TestCasesVarType.test_05_multiple(82): Test
TestCasesVarType.test_01_SNP(58): Test
TestCasesVarType.test_02_MNP(64): Test
TestCasesVarType.test_03_INS(70): Test
TestCasesVarType.test_04_DEL(76): Test
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.071 s - in org.snpsift.tests.unit.TestCasesVarType
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.007 s - in org.snpsift.tests.unit.TestCasesVarType
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameSnp
DataFrame: SNP_A, size: 100, current index: 100, memory: 63.4 KB
Field types:
@@ -3153,9 +3189,9 @@
98 47093 | C | T | E | null | 653352657 | true | WUADUERWVVTEILAAAWWEQGIIUKQTGFVSEPVTJSEWOEWXDUVMQMTIHNQPTSFSEQDBHZBNESFTNMMBHTCZRTQJGILVEE | null | 0.08956523678408113 | QTH |
99 47588 | C | T | Z | null | 1873761820 | false | YNJMWKISSQSPVODXUFKNLGZUIAZNNDFNUFAVMYECUHCAZJBYCLWWKTSGVR | null | 0.9680541190017328 | UCFAOCDFSUNIOOVESGTIPFVKUARMUBGZXYUKKFAFXYZOHHJFVMANHSBRDCSOPTTCSZJSNBGPIFIBAHZYTPM |
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.143 s - in org.snpsift.tests.unit.TestCasesDataFrameSnp
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.snpsift.tests.unit.TestCasesDataFrameSnp
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnChar
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.268 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnChar
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.855 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnChar
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameMixed
DataFrame: MIXED, size: 100, current index: 100, memory: 63.4 KB
Field types:
@@ -3268,7 +3304,7 @@
98 50305 | GGA | AAGG | G | null | -1078219233 | null | LOOZKHCWJZYEZKSPMSDXYJXODFUCNQJPJJQLSMLNNQFYIWKZIBFJARVKVELGNMJBSLVSOJJPATNF | null | 0.7680804977882877 | null |
99 50789 | CTCC | TGATA | N | null | -1627198920 | false | JAJASVDEOFQ | null | 0.5578843763975981 | GYRGQQXTQSITYGVHCIJQYUMGDLDKITYVVNHWOBSZWJLXTOEH |
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.01 s - in org.snpsift.tests.unit.TestCasesDataFrameMixed
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.003 s - in org.snpsift.tests.unit.TestCasesDataFrameMixed
[INFO] Running org.snpsift.tests.unit.TestCasesExtractFields
TestCasesExtractFields.test_31_ann(291): Test
TestCasesExtractFields.test_00(71): Test
@@ -3305,21 +3341,21 @@
TestCasesExtractFields.test_33(312): Test
TestCasesExtractFields.test_34(323): Test
TestCasesExtractFields.test_35(340): Test
-[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.309 s - in org.snpsift.tests.unit.TestCasesExtractFields
+[INFO] Tests run: 35, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.091 s - in org.snpsift.tests.unit.TestCasesExtractFields
[INFO] Running org.snpsift.tests.unit.TestCasesGeneSets
TestCasesGeneSets.test_01(25): Test
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.069 s - in org.snpsift.tests.unit.TestCasesGeneSets
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.027 s - in org.snpsift.tests.unit.TestCasesGeneSets
[INFO] Running org.snpsift.tests.unit.TestCasesGt
TestCasesGt.test_01(25): Test
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.43 s - in org.snpsift.tests.unit.TestCasesGt
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.055 s - in org.snpsift.tests.unit.TestCasesGt
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnFloat
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 3.31 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnFloat
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.558 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnFloat
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnInt
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.64 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnInt
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.17 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnInt
[INFO] Running org.snpsift.tests.unit.TestCasesHwe
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 s - in org.snpsift.tests.unit.TestCasesHwe
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.snpsift.tests.unit.TestCasesHwe
[INFO] Running org.snpsift.tests.unit.TestCasesPosIndex
-[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesPosIndex
+[INFO] Tests run: 6, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.tests.unit.TestCasesPosIndex
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameDel
DataFrame: DEL, size: 100, current index: 100, memory: 63.4 KB
Field types:
@@ -3432,7 +3468,7 @@
98 49907 | CAC | | P | null | 966658647 | true | KGDJSHWQNTLSEYGZ | null | 0.6885368220839251 | GTPFQOWDDNZNFTEUCOAEOMVYXBUMZTNLV |
99 50128 | CA | | E | null | 128095220 | false | NUJYTDVTSDBWKWGYBDKAHAQERJYIGNHYAUFUMIMLNOFPVQJAFDXGIRWIXOBXA | null | 0.4811475357641687 | ZGKNAOXKXJTBFDIJHRUHLXSCTNALYGQVYKSHPRPBNLLZYRIMNEOBUKWLLZRFRXCBJ |
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesDataFrameDel
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.006 s - in org.snpsift.tests.unit.TestCasesDataFrameDel
[INFO] Running org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache
TestCasesDbNsfp.test_01(113): Test
TestCasesDbNsfp.test_02(138): Test
@@ -3440,18 +3476,18 @@
TestCasesDbNsfp.test_04(179): Test
TestCasesDbNsfp.test_05(200): Test
TestCasesDbNsfp.test_06(223): Test
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 28.853 s - in org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 11.96 s - in org.snpsift.tests.unit.TestCasesDbNsfpDeleteCache
[INFO] Running org.snpsift.tests.unit.TestCasesSort
TestCasesSort.test_01(30): Test
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesSort
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesSort
[INFO] Running org.snpsift.tests.unit.TestCasesVariantDatabase
1 1000 . A T . . ZZZ_FIELD_FLOAT=3.14;ZZZ_FIELD_STRING=Value1;ZZZ_FIELD_FLAG=false;ZZZ_FIELD_INT=123
[ZZZ_FIELD_FLOAT, ZZZ_FIELD_FLAG, ZZZ_FIELD_INT, ZZZ_FIELD_STRING]
[FIELD_FLOAT, FIELD_STRING, FIELD_FLAG, FIELD_INT]
-[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.059 s - in org.snpsift.tests.unit.TestCasesVariantDatabase
+[INFO] Tests run: 9, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.017 s - in org.snpsift.tests.unit.TestCasesVariantDatabase
[INFO] Running org.snpsift.tests.unit.TestCasesVcfCheck
TestCasesVcfCheck.test_01(18): Test
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.13 s - in org.snpsift.tests.unit.TestCasesVcfCheck
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.002 s - in org.snpsift.tests.unit.TestCasesVcfCheck
[INFO] Running org.snpsift.tests.unit.TestCasesFilter
TestCasesFilter.test_57_short_circuit_AND_OR_operators(1724): Test
TestCasesFilter.test_32_ann(988): Test
@@ -3521,10 +3557,10 @@
TestCasesFilter.test_27_ann2(812): Test
TestCasesFilter.test_26_ann(721): Test
TestCasesFilter.test_27_ann(778): Test
-[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.014 s - in org.snpsift.tests.unit.TestCasesFilter
+[INFO] Tests run: 68, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.978 s - in org.snpsift.tests.unit.TestCasesFilter
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnString
DataFrameColumnString.resize(76): Converting column 'Test' to EnumArray. Found 6 enums found. Size before: 44 B, after: 5 B
-[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 75.104 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnString
+[INFO] Tests run: 5, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 20.087 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnString
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameMnp
DataFrame: MNP, size: 100, current index: 100, memory: 63.4 KB
Field types:
@@ -3637,7 +3673,7 @@
98 49944 | TAAC | CGCA | G | null | -1858433447 | true | RVKVELGN | null | 0.8010342281968461 | IVYJCJCARHWGLTWGVOVBBSKLOOZKHCWJZYEZKSPMSDXYJXODFUCNQJPJJQLSMLNNQFYIWKZIB |
99 50194 | CTT | TAC | Y | null | -944159107 | true | QYFRYGYRGQQXTQSITYGVHCIJQYUMGDLDKITYVVNHWOBSZWJLXTOEHBWLJAJASVDEOFQVPOEGNJ | null | 0.06701482985829554 | YWMZAJHDQZT |
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.001 s - in org.snpsift.tests.unit.TestCasesDataFrameMnp
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.008 s - in org.snpsift.tests.unit.TestCasesDataFrameMnp
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameIns
DataFrame: INS, size: 100, current index: 100, memory: 63.4 KB
Field types:
@@ -3750,9 +3786,9 @@
98 52327 | | ATCAGG | K | null | null | false | UBYREHOBNQZAXRCSAFUCKBVTXSFZIREOPSNYURKLHJCGPENFCMKHHRQKKZSZXYRELEZOLEJKZFB | null | 0.5758661835439116 | JHJMNUZVVGBGRNL |
99 52862 | | TCGGGA | I | null | -1934920832 | false | OHYE | null | 0.6240226122495972 | UIHQBODOZVZMZKNJIVKSVNASIVINPVYVOOFJZLLPJAFKPFDVHROQPHOPRLLGYJFDTJWMSIQXMEWEAZFG |
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.024 s - in org.snpsift.tests.unit.TestCasesDataFrameIns
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesDataFrameIns
[INFO] Running org.snpsift.tests.unit.TestCasesFilterALL
-[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.122 s - in org.snpsift.tests.unit.TestCasesFilterALL
+[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.035 s - in org.snpsift.tests.unit.TestCasesFilterALL
[INFO] Running org.snpsift.tests.unit.TestCasesAnnotate
TestCasesAnnotate.test_31_annotate_minimal_representation_db(642): Test
TestCasesAnnotate.test_29_repeated_IDs(618): Test
@@ -3796,7 +3832,7 @@
TestCasesAnnotate.test_34_dbStartsOnDifferentChromo(676): Test
TestCasesAnnotate.test_23_allele_specific_annotation_missing_R(491): Test
TestCasesAnnotate.test_27_repeat_db_entry(580): Test
-[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 75.63 s - in org.snpsift.tests.unit.TestCasesAnnotate
+[INFO] Tests run: 42, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 22.622 s - in org.snpsift.tests.unit.TestCasesAnnotate
[INFO] Running org.snpsift.tests.unit.TestCasesDbNsfp
TestCasesDbNsfp.test_01(113): Test
TestCasesDbNsfp.test_02(138): Test
@@ -3804,7 +3840,7 @@
TestCasesDbNsfp.test_04(179): Test
TestCasesDbNsfp.test_05(200): Test
TestCasesDbNsfp.test_06(223): Test
-[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 18.941 s - in org.snpsift.tests.unit.TestCasesDbNsfp
+[INFO] Tests run: 11, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.909 s - in org.snpsift.tests.unit.TestCasesDbNsfp
[INFO] Running org.snpsift.tests.unit.TestCasesGwasCatalog
TestCasesGwasCatalog.test_01(34): Test
WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos '19:16185558' already exists
@@ -3835,11 +3871,11 @@
WARNING_DUPLICATE_PRIMARY_KEY: GwasCatalog entry chr:pos ':-1' already exists
WARNING_DUPLICATE_PRIMARY_KEY: Too many 'WARNING_DUPLICATE_PRIMARY_KEY' warnings, no further warnings will be shown.
TestCasesGwasCatalog.test_02(50): Test
-[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 4.841 s - in org.snpsift.tests.unit.TestCasesGwasCatalog
+[INFO] Tests run: 2, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.964 s - in org.snpsift.tests.unit.TestCasesGwasCatalog
[INFO] Running org.snpsift.tests.unit.TestCasesDataFrameColumnLong
-[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 5.6 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnLong
+[INFO] Tests run: 3, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.277 s - in org.snpsift.tests.unit.TestCasesDataFrameColumnLong
[INFO] Running org.snpsift.tests.unit.TestCasesBoolArray
-[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 2.28 s - in org.snpsift.tests.unit.TestCasesBoolArray
+[INFO] Tests run: 7, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.526 s - in org.snpsift.tests.unit.TestCasesBoolArray
[INFO] Running org.snpsift.tests.unit.TestCasesLd
[INFO] Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0 s - in org.snpsift.tests.unit.TestCasesLd
[INFO]
@@ -3850,8 +3886,8 @@
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 08:13 min
-[INFO] Finished at: 2025-02-17T07:01:33-12:00
+[INFO] Total time: 03:38 min
+[INFO] Finished at: 2026-03-23T15:31:05+14:00
[INFO] ------------------------------------------------------------------------
create-stamp debian/debhelper-build-stamp
dh_prep
@@ -3875,8 +3911,8 @@
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
-[INFO] Total time: 1.950 s
-[INFO] Finished at: 2025-02-17T07:01:40-12:00
+[INFO] Total time: 0.646 s
+[INFO] Finished at: 2026-03-23T15:31:08+14:00
[INFO] ------------------------------------------------------------------------
mh_resolve_dependencies --non-interactive --offline --build -plibsnpsift-java --javadoc --base-directory=/build/reproducible-path/snpsift-5.2.e\+dfsg --non-explore
Failed to parse /usr/share/maven-repo/org/biojava/biojava-structure/6.x/biojava-structure-6.x.pom
@@ -3976,16 +4012,16 @@
dh_missing
dh_installdeb
dh_gencontrol
-dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
-dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined
dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${java:Depends} unused, but is defined
dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package libsnpsift-java: substitution variable ${maven:DocDepends} unused, but is defined
+dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:CompileDepends} unused, but is defined
+dpkg-gencontrol: warning: package libsnpsift-java-doc: substitution variable ${maven:Depends} unused, but is defined
dh_md5sums
dh_builddeb
dpkg-deb: building package 'libsnpsift-java' in '../libsnpsift-java_5.2.e+dfsg-2_all.deb'.
-dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.2.e+dfsg-2_all.deb'.
dpkg-deb: building package 'snpsift' in '../snpsift_5.2.e+dfsg-2_all.deb'.
+dpkg-deb: building package 'libsnpsift-java-doc' in '../libsnpsift-java-doc_5.2.e+dfsg-2_all.deb'.
dpkg-genbuildinfo --build=binary -O../snpsift_5.2.e+dfsg-2_arm64.buildinfo
dpkg-genchanges --build=binary -O../snpsift_5.2.e+dfsg-2_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
@@ -3993,12 +4029,14 @@
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/557284/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/557284/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/1865035 and its subdirectories
-I: Current time: Mon Feb 17 07:02:36 -12 2025
-I: pbuilder-time-stamp: 1739818956
+I: removing directory /srv/workspace/pbuilder/557284 and its subdirectories
+I: Current time: Mon Mar 23 15:31:44 +14 2026
+I: pbuilder-time-stamp: 1774229504