Diff of the two buildlogs:

--
--- b1/build.log	2025-02-09 00:35:23.882103684 +0000
+++ b2/build.log	2025-02-09 00:42:00.900129373 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Fri Mar 13 18:52:01 -12 2026
-I: pbuilder-time-stamp: 1773471121
+I: Current time: Sun Feb  9 14:35:26 +14 2025
+I: pbuilder-time-stamp: 1739061326
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -25,52 +25,84 @@
 dpkg-source: info: applying fix-privacy-breach.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/3836458/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/510437/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 00:35 /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/510437/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/510437/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='3450fbe1e14741ea83318b3d58254ae5'
-  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='3836458'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=bec78ca02d524fb5bd24fe5342e94458
+  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=510437
   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.YO30Kj1W/pbuilderrc_N3x0 --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.YO30Kj1W/b1 --logfile b1/build.log abyss_2.3.10-1.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.YO30Kj1W/pbuilderrc_gD3w --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.YO30Kj1W/b2 --logfile b2/build.log abyss_2.3.10-1.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/3836458/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/510437/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -319,7 +351,7 @@
 Get: 191 http://deb.debian.org/debian trixie/main arm64 libtext-multimarkdown-perl all 1.000035-3 [28.5 kB]
 Get: 192 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
 Get: 193 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
-Fetched 148 MB in 1s (153 MB/s)
+Fetched 148 MB in 1s (259 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package liblocale-gettext-perl.
 (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.)
@@ -950,8 +982,8 @@
 Setting up tzdata (2024b-6) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Sat Mar 14 06:52:34 UTC 2026.
-Universal Time is now:  Sat Mar 14 06:52:34 UTC 2026.
+Local time is now:      Sun Feb  9 00:36:00 UTC 2025.
+Universal Time is now:  Sun Feb  9 00:36:00 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libboost-serialization1.83.0:arm64 (1.83.0-4) ...
@@ -1132,7 +1164,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/abyss-2.3.10/ && 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  > ../abyss_2.3.10-1_source.changes
+I: user script /srv/workspace/pbuilder/510437/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/510437/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/abyss-2.3.10/ && 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  > ../abyss_2.3.10-1_source.changes
 dpkg-buildpackage: info: source package abyss
 dpkg-buildpackage: info: source version 2.3.10-1
 dpkg-buildpackage: info: source distribution unstable
@@ -1180,8 +1216,8 @@
 checking whether make supports the include directive... yes (GNU style)
 checking whether make supports nested variables... yes
 checking xargs -n works... yes
-checking whether UID '1111' is supported by ustar format... yes
-checking whether GID '1111' is supported by ustar format... yes
+checking whether UID '2222' is supported by ustar format... yes
+checking whether GID '2222' is supported by ustar format... yes
 checking how to create a ustar tar archive... gnutar
 checking dependency style of g++ -std=c++11... none
 checking for gawk... (cached) mawk
@@ -1430,10 +1466,10 @@
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-DB.o `test -f 'DB.cc' || echo './'`DB.cc
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o abyss_db_csv-db-csv.o `test -f 'db-csv.cc' || echo './'`db-csv.cc
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o libdb_a-DB.o `test -f 'DB.cc' || echo './'`DB.cc
-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm 
 rm -f libdb.a
 ar cr libdb.a libdb_a-DB.o ../Common/libcommon_a-ContigID.o ../Common/libcommon_a-Fcontrol.o ../Common/libcommon_a-Histogram.o ../Common/libcommon_a-Kmer.o ../Common/libcommon_a-Log.o ../Common/libcommon_a-Options.o ../Common/libcommon_a-Sequence.o ../Common/libcommon_a-SignalHandler.o ../Common/libcommon_a-Timer.o ../Common/libcommon_a-Uncompress.o ../Common/libcommon_a-city.o
 ranlib libdb.a
+g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-db-csv abyss_db_csv-DB.o abyss_db_csv-db-csv.o -lsqlite3 -ldl -lm 
 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/DataBase'
 Making all in FMIndex
 make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/FMIndex'
@@ -1465,12 +1501,6 @@
 gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o parameters.o parameters.c
 gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o prob.o prob.c
 gcc -DHAVE_CONFIG_H -I. -I..   -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o translate.o translate.c
-alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
-   15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
-      |                    ^~~~~~~~~~~~~~
-alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
-   13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
-      |                    ^~~~~~~~~~~
 assemble.c:40:20: warning: inline function 'align_diag' declared but never defined
    40 | extern inline char align_diag(struct alignment *algn, struct scr_matrix *smatrix, struct diag* dg);
       |                    ^~~~~~~~~~
@@ -1486,6 +1516,15 @@
 assemble.c:13:20: warning: inline function 'calc_weight' declared but never defined
    13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
       |                    ^~~~~~~~~~~
+alig.c:15:20: warning: inline function 'calc_ov_weight' declared but never defined
+   15 | extern inline void calc_ov_weight(struct diag* dg, struct diag_col *dcol, struct scr_matrix* smatrix,
+      |                    ^~~~~~~~~~~~~~
+alig.c:13:20: warning: inline function 'calc_weight' declared but never defined
+   13 | extern inline void calc_weight(struct diag* dg, struct scr_matrix* smatrix,
+      |                    ^~~~~~~~~~~
+diag.c:1456:17: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
+ 1456 |                 real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
+      |                 ^~~~~~~~~~~~~~~~
 io.c: In function 'read_scr_matrix':
 io.c:270:17: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
   270 |                 fscanf( fp, "%i", &is);
@@ -1497,9 +1536,6 @@
 io.c:371:7: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result]
   371 |       fscanf( fp, "%li %li %Le\n", &ti,&tscr,&weight );
       |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-diag.c:1456:17: warning: 'real_calc_weight' is static but used in inline function 'find_diags_dyn' which is not static
- 1456 |                 real_calc_weight(dg, smatrix, pdist,1,tmp_dist,algn);
-      |                 ^~~~~~~~~~~~~~~~
 rm -f libdialign.a
 ar cr libdialign.a alig.o assemble.o diag.o io.o orf.o parameters.o prob.o translate.o 
 ranlib libdialign.a
@@ -1536,8 +1572,8 @@
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-NetworkSequenceCollection.o `test -f 'NetworkSequenceCollection.cpp' || echo './'`NetworkSequenceCollection.cpp
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-MessageBuffer.o `test -f 'MessageBuffer.cpp' || echo './'`MessageBuffer.cpp
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -DPAIRED_DBG -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o abyss_paired_dbg_mpi-Messages.o `test -f 'Messages.cpp' || echo './'`Messages.cpp
-g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
 g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o ABYSS-P ABYSS_P-parallelAbyss.o ABYSS_P-CommLayer.o ABYSS_P-NetworkSequenceCollection.o ABYSS_P-MessageBuffer.o ABYSS_P-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
+g++ -std=c++11 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations  -L/usr/lib/aarch64-linux-gnu/openmpi/lib    -Wl,-z,relro -Wl,-z,now -o abyss-paired-dbg-mpi abyss_paired_dbg_mpi-parallelAbyss.o abyss_paired_dbg_mpi-CommLayer.o abyss_paired_dbg_mpi-NetworkSequenceCollection.o abyss_paired_dbg_mpi-MessageBuffer.o abyss_paired_dbg_mpi-Messages.o ../Assembly/libassembly.a ../Common/libcommon.a ../DataLayer/libdatalayer.a ../DataBase/libdb.a -lsqlite3 -ldl -lm  -lmpi  -ldl -lm 
 make[4]: Leaving directory '/build/reproducible-path/abyss-2.3.10/Parallel'
 Making all in Bloom
 make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Bloom'
@@ -1649,7 +1685,7 @@
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I..  -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -Wno-deprecated-declarations -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp
 In file included from ../Graph/GraphIO.h:8,
-                 from PathConsensus.cpp:16:
+                 from MergeContigs.cpp:13:
 ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
 ../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
@@ -1663,9 +1699,9 @@
 ../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
    33 |                 return out << dot_writer(g);
       |                        ~~~~^~~~~~~~~~~~~~~~
-PathConsensus.cpp:999:14:   required from here
-  999 |                 write_graph(fout, g, PROGRAM, commandLine);
-      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+MergeContigs.cpp:428:13:   required from here
+  428 |         write_graph(fout, g, PROGRAM, commandLine);
+      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
    44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
       |                                           ^~
@@ -1673,7 +1709,7 @@
    44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
       |                                                ~~~^~~~~~~~~~~~~~~~~~~
 In file included from ../Graph/GraphIO.h:8,
-                 from MergeContigs.cpp:13:
+                 from PathConsensus.cpp:16:
 ../Graph/DotIO.h: In instantiation of 'void write_edges(std::ostream&, const Graph&, typename boost::graph_traits<Graph>::vertex_descriptor, const EdgeProp*) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; EdgeProp = Distance; std::ostream = std::basic_ostream<char>; typename boost::graph_traits<Graph>::vertex_descriptor = ContigNode]':
 ../Graph/DotIO.h:110:14:   required from 'std::ostream& write_dot(std::ostream&, const Graph&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
   110 |                 write_edges(out, g, *u, (edge_property_type*)NULL);
@@ -1687,9 +1723,9 @@
 ../Graph/GraphIO.h:33:14:   required from 'std::ostream& write_graph(std::ostream&, const Graph&, const std::string&, const std::string&) [with Graph = ContigGraph<DirectedGraph<ContigProperties, Distance> >; std::ostream = std::basic_ostream<char>; std::string = std::__cxx11::basic_string<char>]'
    33 |                 return out << dot_writer(g);
       |                        ~~~~^~~~~~~~~~~~~~~~
-MergeContigs.cpp:428:13:   required from here
-  428 |         write_graph(fout, g, PROGRAM, commandLine);
-      |         ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+PathConsensus.cpp:999:14:   required from here
+  999 |                 write_graph(fout, g, PROGRAM, commandLine);
+      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ../Graph/DotIO.h:44:43: warning: possibly dangling reference to a temporary [-Wdangling-reference]
    44 |                 const edge_property_type& ep = get(edge_bundle, g, e);
       |                                           ^~
@@ -2195,12 +2231,12 @@
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest_main.o `test -f 'src/gtest_main.cc' || echo './'`src/gtest_main.cc
 g++ -std=c++11 -DHAVE_CONFIG_H -I. -I../..  -I../.. -isystem ../../vendor/gtest-1.7.0/include -I/build/reproducible-path/abyss-2.3.10  -isystem/usr/lib/aarch64-linux-gnu/openmpi/include    -Wdate-time -D_FORTIFY_SOURCE=2 -isystem/build/reproducible-path/abyss-2.3.10/boost_1_56_0 -Wall -Wextra -Werror -Wno-missing-field-initializers -Wno-uninitialized -Wno-error=unused-result -g -O2 -ffile-prefix-map=/build/reproducible-path/abyss-2.3.10=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=dangling-reference -c -o src/libgtest_main_a-gtest-all.o `test -f 'src/gtest-all.cc' || echo './'`src/gtest-all.cc
-rm -f libgtest.a
-ar cr libgtest.a src/libgtest_a-gtest-all.o 
-ranlib libgtest.a
 rm -f libgtest_main.a
 ar cr libgtest_main.a src/libgtest_main_a-gtest_main.o src/libgtest_main_a-gtest-all.o 
 ranlib libgtest_main.a
+rm -f libgtest.a
+ar cr libgtest.a src/libgtest_a-gtest-all.o 
+ranlib libgtest.a
 make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
 make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10/vendor/gtest-1.7.0'
 Making check in Unittest
@@ -2279,40 +2315,40 @@
 make  check-TESTS
 make[3]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
 make[4]: Entering directory '/build/reproducible-path/abyss-2.3.10/Unittest'
-PASS: common_histogram
 PASS: common_stringutil
-PASS: common_kmer
+PASS: common_histogram
 PASS: common_bitutil
 PASS: common_KmerIterator
 PASS: common_sequence
-PASS: Konnector_DBGBloomAlgorithms
-PASS: common_sam
-PASS: common_sam_ssq
 PASS: BloomFilter
+PASS: common_kmer
+PASS: common_sam
+PASS: graph_ConstrainedBFSVisitor
 PASS: Konnector_DBGBloom
+PASS: Konnector_DBGBloomAlgorithms
 PASS: graph_ConstrainedBidiBFSVisitor
-PASS: graph_ConstrainedBFSVisitor
+PASS: common_sam_ssq
 PASS: graph_BidirectionalBFS
-PASS: graph_AllPathsSearch
 PASS: graph_ExtendPath
-PASS: PairedDBG_KmerPair
+PASS: graph_AllPathsSearch
 PASS: graph_UndirectedGraph
+PASS: graph_DotIO
 PASS: graph_HashGraph
+PASS: PairedDBG_KmerPair
 PASS: Konnector_konnector
-PASS: graph_DotIO
-PASS: PairedDBG_Dinuc
 PASS: PairedDBG_BranchRecord
+PASS: PairedDBG_Dinuc
 PASS: BloomDBG_BloomDBG
-PASS: BloomDBG_RollingHash
 PASS: BloomDBG_RollingHashIterator
-PASS: BloomDBG_HashAgnosticCascadingBloom
-PASS: BloomDBG_CountingBloomFilter
-PASS: BloomDBG_RollingBloomDBG
-PASS: BloomDBG_MaskedKmer
-PASS: DBG_LoadAlgorithm
+PASS: BloomDBG_RollingHash
 PASS: BloomDBG_SpacedSeed
 PASS: BloomDBG_LightweightKmer
+PASS: BloomDBG_RollingBloomDBG
+PASS: BloomDBG_HashAgnosticCascadingBloom
+PASS: BloomDBG_MaskedKmer
+PASS: BloomDBG_CountingBloomFilter
 PASS: PairedDBG_LoadAlgorithm
+PASS: DBG_LoadAlgorithm
 ============================================================================
 Testsuite summary for ABySS 2.3.10
 ============================================================================
@@ -2651,10 +2687,10 @@
 make[3]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
 make[2]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
 mkdir -p debian/tmp/usr/share/man/man1
-PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
+PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \
      -n "Estimate distances between contigs using paired-end alignments." \
      DistanceEst > debian/tmp/usr/share/man/man1/DistanceEst.1
-PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games help2man --no-info \
+PATH=debian/tmp/usr/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path help2man --no-info \
      -n "Fill the paired-end fields of SAM alignments" abyss-fixmate \
      > debian/tmp/usr/share/man/man1/abyss-fixmate.1
 make[1]: Leaving directory '/build/reproducible-path/abyss-2.3.10'
@@ -2695,12 +2731,14 @@
 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/510437/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/510437/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/3836458 and its subdirectories
-I: Current time: Fri Mar 13 18:58:20 -12 2026
-I: pbuilder-time-stamp: 1773471500
+I: removing directory /srv/workspace/pbuilder/510437 and its subdirectories
+I: Current time: Sun Feb  9 14:41:59 +14 2025
+I: pbuilder-time-stamp: 1739061719