Diff of the two buildlogs:

--
--- b1/build.log	2024-01-12 05:56:56.842881260 +0000
+++ b2/build.log	2024-01-12 06:05:10.464760303 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Thu Feb 13 00:16:59 -12 2025
-I: pbuilder-time-stamp: 1739449019
+I: Current time: Fri Jan 12 19:56:59 +14 2024
+I: pbuilder-time-stamp: 1705039019
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
 I: copying local configuration
@@ -28,49 +28,81 @@
 dpkg-source: info: applying IONiseR.Rmd-fix.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/2110370/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos11-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Jan 12 05:57 /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/3260084/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='amd64'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16 '
-  DISTRIBUTION='bookworm'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.15(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 '
+  DIRSTACK=()
+  DISTRIBUTION=bookworm
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='a04b4faf57224aa49215f73dc86ab3df'
-  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='2110370'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=e88b4052cde44708a438e0dc0e99512e
+  LANG=C
+  LANGUAGE=et_EE:et
+  LC_ALL=C
+  MACHTYPE=x86_64-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=3260084
   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.EcYuqNCO/pbuilderrc_Na8I --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.EcYuqNCO/b1 --logfile b1/build.log r-bioc-ioniser_2.22.0+dfsg-1.dsc'
-  SUDO_GID='110'
-  SUDO_UID='105'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://85.184.249.68:3128'
+  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.EcYuqNCO/pbuilderrc_m3Qe --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.EcYuqNCO/b2 --logfile b2/build.log r-bioc-ioniser_2.22.0+dfsg-1.dsc'
+  SUDO_GID=111
+  SUDO_UID=106
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://78.137.99.97:3128
 I: uname -a
-  Linux ionos5-amd64 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-17-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) x86_64 GNU/Linux
 I: ls -l /bin
   total 5632
   -rwxr-xr-x 1 root root 1265648 Apr 23  2023 bash
@@ -128,15 +160,15 @@
   -rwxr-xr-x 1 root root   52112 Sep 20  2022 readlink
   -rwxr-xr-x 1 root root   72752 Sep 20  2022 rm
   -rwxr-xr-x 1 root root   56240 Sep 20  2022 rmdir
-  -rwxr-xr-x 1 root root   27560 Jul 28  2023 run-parts
+  -rwxr-xr-x 1 root root   27560 Jul 28 23:46 run-parts
   -rwxr-xr-x 1 root root  126424 Jan  5  2023 sed
-  lrwxrwxrwx 1 root root       4 Jan  5  2023 sh -> dash
+  lrwxrwxrwx 1 root root       9 Jan 12 05:57 sh -> /bin/bash
   -rwxr-xr-x 1 root root   43888 Sep 20  2022 sleep
   -rwxr-xr-x 1 root root   85008 Sep 20  2022 stty
   -rwsr-xr-x 1 root root   72000 Mar 23  2023 su
   -rwxr-xr-x 1 root root   39824 Sep 20  2022 sync
   -rwxr-xr-x 1 root root  531984 Apr  6  2023 tar
-  -rwxr-xr-x 1 root root   14520 Jul 28  2023 tempfile
+  -rwxr-xr-x 1 root root   14520 Jul 28 23:46 tempfile
   -rwxr-xr-x 1 root root  109616 Sep 20  2022 touch
   -rwxr-xr-x 1 root root   35664 Sep 20  2022 true
   -rwxr-xr-x 1 root root   14568 Mar 23  2023 ulockmgr_server
@@ -156,7 +188,7 @@
   -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/2110370/tmp/hooks/D02_print_environment finished
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -585,7 +617,7 @@
 Get: 355 http://deb.debian.org/debian bookworm/main amd64 r-cran-markdown all 1.5+dfsg-1 [121 kB]
 Get: 356 http://deb.debian.org/debian bookworm/main amd64 r-cran-purrr amd64 1.0.1-1 [507 kB]
 Get: 357 http://deb.debian.org/debian bookworm/main amd64 r-cran-tidyr amd64 1.3.0-1 [1183 kB]
-Fetched 385 MB in 5s (80.8 MB/s)
+Fetched 385 MB in 52s (7343 kB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 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 ... 18148 files and directories currently installed.)
@@ -1720,8 +1752,8 @@
 Setting up tzdata (2023c-5+deb12u1) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Thu Feb 13 12:17:54 UTC 2025.
-Universal Time is now:  Thu Feb 13 12:17:54 UTC 2025.
+Local time is now:      Fri Jan 12 06:00:58 UTC 2024.
+Universal Time is now:  Fri Jan 12 06:00:58 UTC 2024.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libpcre3:amd64 (2:8.39-15) ...
@@ -2070,7 +2102,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/r-bioc-ioniser-2.22.0+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  > ../r-bioc-ioniser_2.22.0+dfsg-1_source.changes
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for bookworm
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/r-bioc-ioniser-2.22.0+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  > ../r-bioc-ioniser_2.22.0+dfsg-1_source.changes
 dpkg-buildpackage: info: source package r-bioc-ioniser
 dpkg-buildpackage: info: source version 2.22.0+dfsg-1
 dpkg-buildpackage: info: source distribution unstable
@@ -2174,12 +2210,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: including full source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/3260084/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/3260084/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/2110370 and its subdirectories
-I: Current time: Thu Feb 13 00:19:58 -12 2025
-I: pbuilder-time-stamp: 1739449198
+I: removing directory /srv/workspace/pbuilder/3260084 and its subdirectories
+I: Current time: Fri Jan 12 20:05:09 +14 2024
+I: pbuilder-time-stamp: 1705039509