Diff of the two buildlogs:

--
--- b1/build.log	2025-01-08 12:01:16.048665726 +0000
+++ b2/build.log	2025-01-08 12:04:42.555257964 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Tue Feb 10 06:22:13 -12 2026
-I: pbuilder-time-stamp: 1770747733
+I: Current time: Thu Jan  9 02:01:19 +14 2025
+I: pbuilder-time-stamp: 1736337679
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
 I: copying local configuration
@@ -32,54 +32,86 @@
 dpkg-source: info: applying make.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/115972/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos12-i386.
+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  8 12:01 /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/46343/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/46343/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='i386'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 '
-  DISTRIBUTION='unstable'
-  HOME='/root'
-  HOST_ARCH='i386'
+  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]="i686-pc-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=i386
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 '
+  DIRSTACK=()
+  DISTRIBUTION=unstable
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=i686
+  HOST_ARCH=i386
   IFS=' 	
   '
-  INVOCATION_ID='3092ab0f8913439ba468f6d58d637d06'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
-  LD_PRELOAD='libeatmydata.so'
-  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='115972'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=b9facd3d719d4bd19c404ee8f05bda0c
+  LANG=C
+  LANGUAGE=de_CH:de
+  LC_ALL=C
+  LD_LIBRARY_PATH=/usr/lib/libeatmydata
+  LD_PRELOAD=libeatmydata.so
+  MACHTYPE=i686-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=46343
   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.bLSPY1bU/pbuilderrc_Vwn8 --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.bLSPY1bU/b1 --logfile b1/build.log phast_1.7+dfsg-2.dsc'
-  SUDO_GID='112'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://213.165.73.152:3128'
+  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.bLSPY1bU/pbuilderrc_SZpb --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.bLSPY1bU/b2 --logfile b2/build.log phast_1.7+dfsg-2.dsc'
+  SUDO_GID=112
+  SUDO_UID=107
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://46.16.76.132:3128
 I: uname -a
-  Linux ionos6-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/115972/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/46343/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -174,7 +206,7 @@
 Get: 43 http://deb.debian.org/debian unstable/main i386 libpcre2-32-0 i386 10.44-5 [246 kB]
 Get: 44 http://deb.debian.org/debian unstable/main i386 libpcre2-posix3 i386 10.44-5 [60.4 kB]
 Get: 45 http://deb.debian.org/debian unstable/main i386 libpcre2-dev i386 10.44-5 [800 kB]
-Fetched 30.8 MB in 0s (87.7 MB/s)
+Fetched 30.8 MB in 1s (61.5 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 ... 19834 files and directories currently installed.)
@@ -373,7 +405,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/phast-1.7+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  > ../phast_1.7+dfsg-2_source.changes
+I: user script /srv/workspace/pbuilder/46343/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for unstable
+I: user script /srv/workspace/pbuilder/46343/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/phast-1.7+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  > ../phast_1.7+dfsg-2_source.changes
 dpkg-buildpackage: info: source package phast
 dpkg-buildpackage: info: source version 1.7+dfsg-2
 dpkg-buildpackage: info: source distribution unstable
@@ -470,7 +506,7 @@
    dh_autoreconf
    dh_auto_configure
    dh_auto_build
-	make -j22 "INSTALL=install --strip-program=true"
+	make -j10 "INSTALL=install --strip-program=true"
 make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
 Type "make package" to create a tarball reflecting the current state of the CVS tree.
 (cd src; make DESTDIR= CLAPACKPATH=/usr/lib )
@@ -1243,17 +1279,17 @@
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c phast_pbs_code.c -o phast_pbs_code.o 
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsEncode.c -o pbsEncode.o 
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsScoreMatrix.c -o pbsScoreMatrix.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c pbsTrain.c -o pbsTrain.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/prequel/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/prequel/../..\" -fno-strict-aliasing -c prequel.c -o prequel.o 
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
@@ -1358,74 +1394,72 @@
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c chooseLines.c -o chooseLines.o 
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c clean_genes.c -o clean_genes.o 
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c consEntropy.c -o consEntropy.o 
-<command-line>: warning: "PHAST_HOME" redefined
-<command-line>: note: this is the location of the previous definition
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c convert_coords.c -o convert_coords.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c display_rate_matrix.c -o display_rate_matrix.o 
-<command-line>: warning: "PHAST_HOME" redefined
-<command-line>: note: this is the location of the previous definition
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c draw_tree.c -o draw_tree.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c eval_predictions.c -o eval_predictions.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_train.c -o hmm_train.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+display_rate_matrix.c: In function 'do_context_dependent_ti_tv':
+display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable]
+  204 |   char tuple_i[mod->order+2], tuple_j[mod->order+2];
+      |        ^~~~~~~
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_tweak.c -o hmm_tweak.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c hmm_view.c -o hmm_view.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelFit.c -o indelFit.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c indelHistory.c -o indelHistory.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c maf_parse.c -o maf_parse.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c makeHKY.c -o makeHKY.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c modFreqs.c -o modFreqs.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_diff.c -o msa_diff.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_split.c -o msa_split.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c msa_view.c -o msa_view.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-display_rate_matrix.c: In function 'do_context_dependent_ti_tv':
-display_rate_matrix.c:204:8: warning: variable 'tuple_i' set but not used [-Wunused-but-set-variable]
-  204 |   char tuple_i[mod->order+2], tuple_j[mod->order+2];
-      |        ^~~~~~~
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o 
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phast.c -o phast.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c phastBias.c -o phastBias.o 
+<command-line>: warning: "PHAST_HOME" redefined
+<command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c refeature.c -o refeature.o 
 msa_view.c: In function 'fill_with_Ns':
 msa_view.c:361:49: warning: pointer targets in passing argument 1 of 'str_re_new' differ in signedness [-Wpointer-sign]
   361 |   pcre2_compile_context* fill_N_re = str_re_new("([[:digit:]]+):([[:digit:]]+)-([[:digit:]]+)");
@@ -1438,21 +1472,19 @@
 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/stringsplus.h:386:56: note: expected 'const unsigned char *' but argument is of type 'char *'
   386 | pcre2_compile_context *str_re_new(const unsigned char *re_str);
       |                                   ~~~~~~~~~~~~~~~~~~~~~^~~~~~
+<command-line>: warning: "PHAST_HOME" redefined
+<command-line>: note: this is the location of the previous definition
 gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c stringiphy.c -o stringiphy.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o 
-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c treeGen.c -o treeGen.o 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
+gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/phast-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/..\" -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Wall -I/build/reproducible-path/phast-1.7+dfsg/src/util/../../include -DPHAST_VERSION=\"v1.6\" -DPHAST_HOME=\"/build/reproducible-path/phast-1.7+dfsg/src/util/../..\" -fno-strict-aliasing -c tree_doctor.c -o tree_doctor.o 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 <command-line>: warning: "PHAST_HOME" redefined
 <command-line>: note: this is the location of the previous definition
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 tree_doctor.c: In function 'main':
 tree_doctor.c:348:19: warning: the comparison will always evaluate as 'true' for the address of 'name' will never be NULL [-Waddress]
   348 |       if (n->name != NULL && n->name[0] != '\0' &&
@@ -1462,23 +1494,27 @@
 /build/reproducible-path/phast-1.7+dfsg/src/../include/phast/trees.h:47:8: note: 'name' declared here
    47 |   char name [STR_MED_LEN];      /**< Name of this node i.e. 'Drosophila 23' usually one of the sequence names */
       |        ^~~~
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/base_evolve base_evolve.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/chooseLines chooseLines.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/consEntropy consEntropy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/convert_coords convert_coords.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/draw_tree draw_tree.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_view hmm_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelFit indelFit.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/indelHistory indelHistory.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/makeHKY makeHKY.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/modFreqs modFreqs.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_diff msa_diff.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_train hmm_train.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phast phast.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/phastBias phastBias.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/refeature refeature.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/stringiphy stringiphy.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/hmm_tweak hmm_tweak.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/all_dists all_dists.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/eval_predictions eval_predictions.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/treeGen treeGen.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
+gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/tree_doctor tree_doctor.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_view msa_view.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
-gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/maf_parse maf_parse.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/msa_split msa_split.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/display_rate_matrix display_rate_matrix.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
 gcc -L/build/reproducible-path/phast-1.7+dfsg/src/util/../../lib   -o /build/reproducible-path/phast-1.7+dfsg/src/util/../../bin/clean_genes clean_genes.o -lphast -llapack -ltmglib -lblas -lc -lm -lpcre2-8 -Wl,-z,relro -Wl,-z,now 
@@ -1537,7 +1573,7 @@
 make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
    debian/rules override_dh_auto_test
 make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
-cd test && PATH=/build/reproducible-path/phast-1.7+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games /usr/bin/make msa_view
+cd test && PATH=/build/reproducible-path/phast-1.7+dfsg/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path /usr/bin/make msa_view
 make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/test'
 *** Testing msa_view ***
 msa_view hmrc.ss -i SS --end 10000 > hmrc.fa
@@ -1565,14 +1601,14 @@
 if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi
 msa_view hmrc.ss --summary -i SS > hmrc_summary
 if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi
--e Passed all tests.
+Passed all tests.
 
 make[2]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg/test'
 make[1]: Leaving directory '/build/reproducible-path/phast-1.7+dfsg'
    create-stamp debian/debhelper-build-stamp
    dh_prep
    dh_auto_install --destdir=debian/phast/
-	make -j22 install DESTDIR=/build/reproducible-path/phast-1.7\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+	make -j10 install DESTDIR=/build/reproducible-path/phast-1.7\+dfsg/debian/phast AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
 make[1]: Entering directory '/build/reproducible-path/phast-1.7+dfsg'
 (cd src; make install DESTDIR=/build/reproducible-path/phast-1.7+dfsg/debian/phast )
 make[2]: Entering directory '/build/reproducible-path/phast-1.7+dfsg/src'
@@ -1615,12 +1651,14 @@
 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/46343/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/46343/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/115972 and its subdirectories
-I: Current time: Tue Feb 10 06:24:14 -12 2026
-I: pbuilder-time-stamp: 1770747854
+I: removing directory /srv/workspace/pbuilder/46343 and its subdirectories
+I: Current time: Thu Jan  9 02:04:41 +14 2025
+I: pbuilder-time-stamp: 1736337881