Diff of the two buildlogs:

--
--- b1/build.log	2025-02-09 00:30:36.715104978 +0000
+++ b2/build.log	2025-02-09 00:32:55.264832200 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Fri Mar 13 18:51:29 -12 2026
-I: pbuilder-time-stamp: 1773471089
+I: Current time: Sun Feb  9 14:30:40 +14 2025
+I: pbuilder-time-stamp: 1739061040
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -28,52 +28,84 @@
 dpkg-source: info: applying ld_as_needed
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3826059/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/436268/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink04-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 00:30 /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/436268/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/436268/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='trixie'
-  HOME='/root'
-  HOST_ARCH='arm64'
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=aarch64
+  HOST_ARCH=arm64
   IFS=' 	
   '
-  INVOCATION_ID='680421646db14bd1b36d57258681f4e1'
-  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='3826059'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=732e10c36ea14861958eca783dd2e942
+  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=436268
   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.8na6N2VT/pbuilderrc_gvpI --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8na6N2VT/b1 --logfile b1/build.log reapr_1.0.18+dfsg-7.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.8na6N2VT/pbuilderrc_An0q --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8na6N2VT/b2 --logfile b2/build.log reapr_1.0.18+dfsg-7.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 codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/3826059/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/436268/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -337,7 +369,7 @@
 Get: 202 http://deb.debian.org/debian trixie/main arm64 smalt arm64 0.7.6-13+b1 [105 kB]
 Get: 203 http://deb.debian.org/debian trixie/main arm64 snpomatic arm64 1.0-7+b1 [74.2 kB]
 Get: 204 http://deb.debian.org/debian trixie/main arm64 tabix arm64 1.20+ds-2 [455 kB]
-Fetched 117 MB in 1s (93.6 MB/s)
+Fetched 117 MB in 0s (240 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package tzdata.
 (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 ... 19956 files and directories currently installed.)
@@ -1005,8 +1037,8 @@
 Setting up tzdata (2024b-6) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Sat Mar 14 06:51:58 UTC 2026.
-Universal Time is now:  Sat Mar 14 06:51:58 UTC 2026.
+Local time is now:      Sun Feb  9 00:31:09 UTC 2025.
+Universal Time is now:  Sun Feb  9 00:31:09 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up zip (3.0-14+b1) ...
@@ -1196,7 +1228,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/reapr-1.0.18+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  > ../reapr_1.0.18+dfsg-7_source.changes
+I: user script /srv/workspace/pbuilder/436268/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/436268/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/reapr-1.0.18+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  > ../reapr_1.0.18+dfsg-7_source.changes
 dpkg-buildpackage: info: source package reapr
 dpkg-buildpackage: info: source version 1.0.18+dfsg-7
 dpkg-buildpackage: info: source distribution unstable
@@ -1311,7 +1347,7 @@
 make[1]: Entering directory '/build/reproducible-path/reapr-1.0.18+dfsg'
 mkdir /build/reproducible-path/reapr-1.0.18+dfsg/debian/test
 ln -s /build/reproducible-path/reapr-1.0.18+dfsg/src/reapr.pl /build/reproducible-path/reapr-1.0.18+dfsg/debian/test/reapr
-PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/build/reproducible-path/reapr-1.0.18+dfsg/src:/build/reproducible-path/reapr-1.0.18+dfsg/debian/test /build/reproducible-path/reapr-1.0.18+dfsg/debian/tests/test-example
+PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path:/build/reproducible-path/reapr-1.0.18+dfsg/src:/build/reproducible-path/reapr-1.0.18+dfsg/debian/test /build/reproducible-path/reapr-1.0.18+dfsg/debian/tests/test-example
 [wgsim] seed = 42
 [wgsim_core] calculating the total length of the reference sequence...
 [wgsim_core] 1 sequences, total length: 1000111
@@ -2292,8 +2328,8 @@
 foo	994610	C	Y	+
 foo	998107	-	T	+
 foo	999725	G	R	+
-[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.3855511.smaltmap.smalt_index foo1.fasta
-# Command line:  smalt index -k 13 -s 2 out.bam.tmp.3855511.smaltmap.smalt_index foo1.fasta
+[REAPR smaltmap] Running: smalt index -k 13 -s 2 out.bam.tmp.450380.smaltmap.smalt_index foo1.fasta
+# Command line:  smalt index -k 13 -s 2 out.bam.tmp.450380.smaltmap.smalt_index foo1.fasta
 # Reading sequences ...
 # Writing sequence set ...
 # Setting up hash index with collisions ...
@@ -2317,8 +2353,8 @@
 # =-=-= End of Hash Index Stats =-=-=
 # Writing table to file ... 
 # smalt: Total elapsed wall clock time: 1 seconds
-[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.3855511.smaltmap.smalt_sample out.bam.tmp.3855511.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
-# Command line:  smalt sample -u 1000 -o out.bam.tmp.3855511.smaltmap.smalt_sample out.bam.tmp.3855511.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
+[REAPR smaltmap] Running: smalt sample -u 1000 -o out.bam.tmp.450380.smaltmap.smalt_sample out.bam.tmp.450380.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
+# Command line:  smalt sample -u 1000 -o out.bam.tmp.450380.smaltmap.smalt_sample out.bam.tmp.450380.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
 # Opening read files ...
 # Reading reference sequences ...
 # Reading hash table ...
@@ -2339,8 +2375,8 @@
 # smalt: Time spent setting up hash index:0 seconds
 # smalt: Time spent mapping reads:2 seconds
 # smalt: Total elapsed wall clock time: 2 seconds
-[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5   -g out.bam.tmp.3855511.smaltmap.smalt_sample -f samsoft out.bam.tmp.3855511.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/'   | samtools view -S -T foo1.fasta -b - > out.bam.tmp.3855511.smaltmap.raw.bam
-# Command line:  smalt map -r 0 -x -y 0.5 -g out.bam.tmp.3855511.smaltmap.smalt_sample -f samsoft out.bam.tmp.3855511.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
+[REAPR smaltmap] Running: smalt map -r 0 -x -y 0.5   -g out.bam.tmp.450380.smaltmap.smalt_sample -f samsoft out.bam.tmp.450380.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq | awk '$1!~/^#/'   | samtools view -S -T foo1.fasta -b - > out.bam.tmp.450380.smaltmap.raw.bam
+# Command line:  smalt map -r 0 -x -y 0.5 -g out.bam.tmp.450380.smaltmap.smalt_sample -f samsoft out.bam.tmp.450380.smaltmap.smalt_index foofq.1.fastq foofq.2.fastq
 # Reading distribution of insert sizes from file ...
 # Sampled histogram
 # Smoothed histogram
@@ -2362,15 +2398,15 @@
 # smalt: Time spent setting up hash index:0 seconds
 # smalt: Time spent mapping reads:11 seconds
 # smalt: Total elapsed wall clock time: 11 seconds
-[REAPR smaltmap] Running: samtools sort out.bam.tmp.3855511.smaltmap.raw.bam -O bam -o out.bam.tmp.3855511.smaltmap.raw.bam.sort.bam
-[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.3855511.smaltmap.raw.bam.sort.bam out.bam.tmp.3855511.smaltmap.rmdup.bam
+[REAPR smaltmap] Running: samtools sort out.bam.tmp.450380.smaltmap.raw.bam -O bam -o out.bam.tmp.450380.smaltmap.raw.bam.sort.bam
+[REAPR smaltmap] Running: samtools rmdup out.bam.tmp.450380.smaltmap.raw.bam.sort.bam out.bam.tmp.450380.smaltmap.rmdup.bam
 [bam_rmdup_core] processing reference foo...
 [bam_rmdup_core] 1 / 10000 = 0.0001 in library '	'
-[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.3855511.smaltmap.header
-[REAPR smaltmap] Running: samtools view -H out.bam.tmp.3855511.smaltmap.rmdup.bam >> out.bam.tmp.3855511.smaltmap.header
-[REAPR smaltmap] Running: samtools reheader out.bam.tmp.3855511.smaltmap.header out.bam.tmp.3855511.smaltmap.rmdup.bam > out.bam
+[REAPR smaltmap] Running: echo "@HD VN:1.0 SO:coordinate" | awk '{OFS="\t"; $1=$1; print}' > out.bam.tmp.450380.smaltmap.header
+[REAPR smaltmap] Running: samtools view -H out.bam.tmp.450380.smaltmap.rmdup.bam >> out.bam.tmp.450380.smaltmap.header
+[REAPR smaltmap] Running: samtools reheader out.bam.tmp.450380.smaltmap.header out.bam.tmp.450380.smaltmap.rmdup.bam > out.bam
 [REAPR smaltmap] Running: samtools index out.bam
-[REAPR smaltmap] Running: rm out.bam.tmp.3855511.smaltmap.*
+[REAPR smaltmap] Running: rm out.bam.tmp.450380.smaltmap.*
 Running reapr version 1.0.18 pipeline:
 reapr foo1.fasta out.bam result
 [REAPR pipeline] Running facheck
@@ -2442,12 +2478,14 @@
 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/436268/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/436268/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/3826059 and its subdirectories
-I: Current time: Fri Mar 13 18:53:35 -12 2026
-I: pbuilder-time-stamp: 1773471215
+I: removing directory /srv/workspace/pbuilder/436268 and its subdirectories
+I: Current time: Sun Feb  9 14:32:54 +14 2025
+I: pbuilder-time-stamp: 1739061174