Diff of the two buildlogs:

--
--- b1/build.log	2021-07-22 07:28:30.588968496 +0000
+++ b2/build.log	2021-07-22 07:33:13.110348651 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Wed Aug 24 01:47:33 -12 2022
-I: pbuilder-time-stamp: 1661348853
+I: Current time: Thu Jul 22 21:28:32 +14 2021
+I: pbuilder-time-stamp: 1626938912
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz]
 I: copying local configuration
@@ -17,7 +17,7 @@
 I: Extracting source
 gpgv: unknown type of key resource 'trustedkeys.kbx'
 gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error
-gpgv: Signature made Sat Oct 27 10:53:18 2018 -12
+gpgv: Signature made Sun Oct 28 12:53:18 2018 +14
 gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 gpgv:                issuer "tille@debian.org"
 gpgv: Can't check signature: No public key
@@ -27,136 +27,170 @@
 dpkg-source: info: unpacking bioperl_1.7.2-3.debian.tar.xz
 I: using fakeroot in build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/11805/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/41996/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
+Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
+Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
+Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
+Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/41996/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/41996/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build'
-  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=''
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.0.3(1)-release'
+  BUILDDIR=/build
+  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=
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='246f576eee1242499e7b93338e5b3548'
-  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='11805'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=5b2ad986eba249eabd0ea38f78bde827
+  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=41996
   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/tmp.Uwj2Jq9kyP/pbuilderrc_oKbd --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Uwj2Jq9kyP/b1 --logfile b1/build.log bioperl_1.7.2-3.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/tmp.Uwj2Jq9kyP/pbuilderrc_ehHn --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.Uwj2Jq9kyP/b2 --logfile b2/build.log bioperl_1.7.2-3.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 5.10.0-0.bpo.7-amd64 #1 SMP Debian 5.10.40-1~bpo10+1 (2021-06-04) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 4.19.0-17-amd64 #1 SMP Debian 4.19.194-3 (2021-07-18) x86_64 GNU/Linux
 I: ls -l /bin
   total 5116
-  -rwxr-xr-x 1 root root 1168776 Apr 17  2019 bash
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bunzip2
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bzcat
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzcmp -> bzdiff
-  -rwxr-xr-x 1 root root    2227 Jul 10  2019 bzdiff
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzegrep -> bzgrep
-  -rwxr-xr-x 1 root root    4877 Jun 24  2019 bzexe
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzfgrep -> bzgrep
-  -rwxr-xr-x 1 root root    3641 Jul 10  2019 bzgrep
-  -rwxr-xr-x 3 root root   38984 Jul 10  2019 bzip2
-  -rwxr-xr-x 1 root root   14328 Jul 10  2019 bzip2recover
-  lrwxrwxrwx 1 root root       6 Jul 10  2019 bzless -> bzmore
-  -rwxr-xr-x 1 root root    1297 Jul 10  2019 bzmore
-  -rwxr-xr-x 1 root root   43744 Feb 28  2019 cat
-  -rwxr-xr-x 1 root root   64320 Feb 28  2019 chgrp
-  -rwxr-xr-x 1 root root   64288 Feb 28  2019 chmod
-  -rwxr-xr-x 1 root root   72512 Feb 28  2019 chown
-  -rwxr-xr-x 1 root root  146880 Feb 28  2019 cp
-  -rwxr-xr-x 1 root root  121464 Jan 17  2019 dash
-  -rwxr-xr-x 1 root root  109408 Feb 28  2019 date
-  -rwxr-xr-x 1 root root   76712 Feb 28  2019 dd
-  -rwxr-xr-x 1 root root   93744 Feb 28  2019 df
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 dir
-  -rwxr-xr-x 1 root root   84288 Jan  9  2019 dmesg
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 dnsdomainname -> hostname
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 domainname -> hostname
-  -rwxr-xr-x 1 root root   39520 Feb 28  2019 echo
-  -rwxr-xr-x 1 root root      28 Jan  7  2019 egrep
-  -rwxr-xr-x 1 root root   35424 Feb 28  2019 false
-  -rwxr-xr-x 1 root root      28 Jan  7  2019 fgrep
-  -rwxr-xr-x 1 root root   68880 Jan  9  2019 findmnt
-  -rwsr-xr-x 1 root root   34896 Apr 22  2020 fusermount
-  -rwxr-xr-x 1 root root  198976 Jan  7  2019 grep
-  -rwxr-xr-x 2 root root    2345 Jan  5  2019 gunzip
-  -rwxr-xr-x 1 root root    6375 Jan  5  2019 gzexe
-  -rwxr-xr-x 1 root root   98048 Jan  5  2019 gzip
-  -rwxr-xr-x 1 root root   26696 Sep 26  2018 hostname
-  -rwxr-xr-x 1 root root   68552 Feb 28  2019 ln
-  -rwxr-xr-x 1 root root   56760 Jul 26  2018 login
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 ls
-  -rwxr-xr-x 1 root root  108624 Jan  9  2019 lsblk
-  -rwxr-xr-x 1 root root   89088 Feb 28  2019 mkdir
-  -rwxr-xr-x 1 root root   68544 Feb 28  2019 mknod
-  -rwxr-xr-x 1 root root   43808 Feb 28  2019 mktemp
-  -rwxr-xr-x 1 root root   43008 Jan  9  2019 more
-  -rwsr-xr-x 1 root root   51280 Jan  9  2019 mount
-  -rwxr-xr-x 1 root root   14408 Jan  9  2019 mountpoint
-  -rwxr-xr-x 1 root root  138728 Feb 28  2019 mv
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 nisdomainname -> hostname
-  lrwxrwxrwx 1 root root      14 Feb 14  2019 pidof -> /sbin/killall5
-  -rwxr-xr-x 1 root root   39616 Feb 28  2019 pwd
-  lrwxrwxrwx 1 root root       4 Apr 17  2019 rbash -> bash
-  -rwxr-xr-x 1 root root   47776 Feb 28  2019 readlink
-  -rwxr-xr-x 1 root root   68416 Feb 28  2019 rm
-  -rwxr-xr-x 1 root root   47776 Feb 28  2019 rmdir
-  -rwxr-xr-x 1 root root   23312 Jan 21  2019 run-parts
-  -rwxr-xr-x 1 root root  122224 Dec 22  2018 sed
-  lrwxrwxrwx 1 root root       4 Aug 23 02:46 sh -> dash
-  -rwxr-xr-x 1 root root   39552 Feb 28  2019 sleep
-  -rwxr-xr-x 1 root root   80672 Feb 28  2019 stty
-  -rwsr-xr-x 1 root root   63568 Jan  9  2019 su
-  -rwxr-xr-x 1 root root   35488 Feb 28  2019 sync
-  -rwxr-xr-x 1 root root  445560 Apr 23  2019 tar
-  -rwxr-xr-x 1 root root   14440 Jan 21  2019 tempfile
-  -rwxr-xr-x 1 root root   97152 Feb 28  2019 touch
-  -rwxr-xr-x 1 root root   35424 Feb 28  2019 true
-  -rwxr-xr-x 1 root root   14328 Apr 22  2020 ulockmgr_server
-  -rwsr-xr-x 1 root root   34888 Jan  9  2019 umount
-  -rwxr-xr-x 1 root root   39584 Feb 28  2019 uname
-  -rwxr-xr-x 2 root root    2345 Jan  5  2019 uncompress
-  -rwxr-xr-x 1 root root  138856 Feb 28  2019 vdir
-  -rwxr-xr-x 1 root root   34896 Jan  9  2019 wdctl
-  -rwxr-xr-x 1 root root     946 Jan 21  2019 which
-  lrwxrwxrwx 1 root root       8 Sep 26  2018 ypdomainname -> hostname
-  -rwxr-xr-x 1 root root    1983 Jan  5  2019 zcat
-  -rwxr-xr-x 1 root root    1677 Jan  5  2019 zcmp
-  -rwxr-xr-x 1 root root    5879 Jan  5  2019 zdiff
-  -rwxr-xr-x 1 root root      29 Jan  5  2019 zegrep
-  -rwxr-xr-x 1 root root      29 Jan  5  2019 zfgrep
-  -rwxr-xr-x 1 root root    2080 Jan  5  2019 zforce
-  -rwxr-xr-x 1 root root    7584 Jan  5  2019 zgrep
-  -rwxr-xr-x 1 root root    2205 Jan  5  2019 zless
-  -rwxr-xr-x 1 root root    1841 Jan  5  2019 zmore
-  -rwxr-xr-x 1 root root    4552 Jan  5  2019 znew
-I: user script /srv/workspace/pbuilder/11805/tmp/hooks/D02_print_environment finished
+  -rwxr-xr-x 1 root root 1168776 Apr 18  2019 bash
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bunzip2
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bzcat
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzcmp -> bzdiff
+  -rwxr-xr-x 1 root root    2227 Jul 11  2019 bzdiff
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzegrep -> bzgrep
+  -rwxr-xr-x 1 root root    4877 Jun 25  2019 bzexe
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzfgrep -> bzgrep
+  -rwxr-xr-x 1 root root    3641 Jul 11  2019 bzgrep
+  -rwxr-xr-x 3 root root   38984 Jul 11  2019 bzip2
+  -rwxr-xr-x 1 root root   14328 Jul 11  2019 bzip2recover
+  lrwxrwxrwx 1 root root       6 Jul 11  2019 bzless -> bzmore
+  -rwxr-xr-x 1 root root    1297 Jul 11  2019 bzmore
+  -rwxr-xr-x 1 root root   43744 Mar  1  2019 cat
+  -rwxr-xr-x 1 root root   64320 Mar  1  2019 chgrp
+  -rwxr-xr-x 1 root root   64288 Mar  1  2019 chmod
+  -rwxr-xr-x 1 root root   72512 Mar  1  2019 chown
+  -rwxr-xr-x 1 root root  146880 Mar  1  2019 cp
+  -rwxr-xr-x 1 root root  121464 Jan 18  2019 dash
+  -rwxr-xr-x 1 root root  109408 Mar  1  2019 date
+  -rwxr-xr-x 1 root root   76712 Mar  1  2019 dd
+  -rwxr-xr-x 1 root root   93744 Mar  1  2019 df
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 dir
+  -rwxr-xr-x 1 root root   84288 Jan 10  2019 dmesg
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 dnsdomainname -> hostname
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 domainname -> hostname
+  -rwxr-xr-x 1 root root   39520 Mar  1  2019 echo
+  -rwxr-xr-x 1 root root      28 Jan  8  2019 egrep
+  -rwxr-xr-x 1 root root   35424 Mar  1  2019 false
+  -rwxr-xr-x 1 root root      28 Jan  8  2019 fgrep
+  -rwxr-xr-x 1 root root   68880 Jan 10  2019 findmnt
+  -rwsr-xr-x 1 root root   34896 Apr 23  2020 fusermount
+  -rwxr-xr-x 1 root root  198976 Jan  8  2019 grep
+  -rwxr-xr-x 2 root root    2345 Jan  6  2019 gunzip
+  -rwxr-xr-x 1 root root    6375 Jan  6  2019 gzexe
+  -rwxr-xr-x 1 root root   98048 Jan  6  2019 gzip
+  -rwxr-xr-x 1 root root   26696 Sep 27  2018 hostname
+  -rwxr-xr-x 1 root root   68552 Mar  1  2019 ln
+  -rwxr-xr-x 1 root root   56760 Jul 27  2018 login
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 ls
+  -rwxr-xr-x 1 root root  108624 Jan 10  2019 lsblk
+  -rwxr-xr-x 1 root root   89088 Mar  1  2019 mkdir
+  -rwxr-xr-x 1 root root   68544 Mar  1  2019 mknod
+  -rwxr-xr-x 1 root root   43808 Mar  1  2019 mktemp
+  -rwxr-xr-x 1 root root   43008 Jan 10  2019 more
+  -rwsr-xr-x 1 root root   51280 Jan 10  2019 mount
+  -rwxr-xr-x 1 root root   14408 Jan 10  2019 mountpoint
+  -rwxr-xr-x 1 root root  138728 Mar  1  2019 mv
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 nisdomainname -> hostname
+  lrwxrwxrwx 1 root root      14 Feb 15  2019 pidof -> /sbin/killall5
+  -rwxr-xr-x 1 root root   39616 Mar  1  2019 pwd
+  lrwxrwxrwx 1 root root       4 Apr 18  2019 rbash -> bash
+  -rwxr-xr-x 1 root root   47776 Mar  1  2019 readlink
+  -rwxr-xr-x 1 root root   68416 Mar  1  2019 rm
+  -rwxr-xr-x 1 root root   47776 Mar  1  2019 rmdir
+  -rwxr-xr-x 1 root root   23312 Jan 22  2019 run-parts
+  -rwxr-xr-x 1 root root  122224 Dec 23  2018 sed
+  lrwxrwxrwx 1 root root       4 Jul 22 21:28 sh -> bash
+  lrwxrwxrwx 1 root root       4 Jul 21 22:24 sh.distrib -> dash
+  -rwxr-xr-x 1 root root   39552 Mar  1  2019 sleep
+  -rwxr-xr-x 1 root root   80672 Mar  1  2019 stty
+  -rwsr-xr-x 1 root root   63568 Jan 10  2019 su
+  -rwxr-xr-x 1 root root   35488 Mar  1  2019 sync
+  -rwxr-xr-x 1 root root  445560 Apr 24  2019 tar
+  -rwxr-xr-x 1 root root   14440 Jan 22  2019 tempfile
+  -rwxr-xr-x 1 root root   97152 Mar  1  2019 touch
+  -rwxr-xr-x 1 root root   35424 Mar  1  2019 true
+  -rwxr-xr-x 1 root root   14328 Apr 23  2020 ulockmgr_server
+  -rwsr-xr-x 1 root root   34888 Jan 10  2019 umount
+  -rwxr-xr-x 1 root root   39584 Mar  1  2019 uname
+  -rwxr-xr-x 2 root root    2345 Jan  6  2019 uncompress
+  -rwxr-xr-x 1 root root  138856 Mar  1  2019 vdir
+  -rwxr-xr-x 1 root root   34896 Jan 10  2019 wdctl
+  -rwxr-xr-x 1 root root     946 Jan 22  2019 which
+  lrwxrwxrwx 1 root root       8 Sep 27  2018 ypdomainname -> hostname
+  -rwxr-xr-x 1 root root    1983 Jan  6  2019 zcat
+  -rwxr-xr-x 1 root root    1677 Jan  6  2019 zcmp
+  -rwxr-xr-x 1 root root    5879 Jan  6  2019 zdiff
+  -rwxr-xr-x 1 root root      29 Jan  6  2019 zegrep
+  -rwxr-xr-x 1 root root      29 Jan  6  2019 zfgrep
+  -rwxr-xr-x 1 root root    2080 Jan  6  2019 zforce
+  -rwxr-xr-x 1 root root    7584 Jan  6  2019 zgrep
+  -rwxr-xr-x 1 root root    2205 Jan  6  2019 zless
+  -rwxr-xr-x 1 root root    1841 Jan  6  2019 zmore
+  -rwxr-xr-x 1 root root    4552 Jan  6  2019 znew
+I: user script /srv/workspace/pbuilder/41996/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -503,7 +537,7 @@
 Get: 223 http://deb.debian.org/debian buster/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB]
 Get: 224 http://deb.debian.org/debian buster/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB]
 Get: 225 http://deb.debian.org/debian buster/main amd64 rename all 1.10-1 [17.2 kB]
-Fetched 49.4 MB in 1s (53.0 MB/s)
+Fetched 49.4 MB in 1s (37.7 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libbsd0:amd64.
 (Reading database ... 
(Reading database ... 5%
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(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 ... 19195 files and directories currently installed.)
@@ -1454,7 +1488,7 @@
 fakeroot is already the newest version (1.23-1).
 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 I: Building the package
-I: Running cd /build/bioperl-1.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b
+I: Running cd /build/bioperl-1.7.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b
 dpkg-buildpackage: info: source package bioperl
 dpkg-buildpackage: info: source version 1.7.2-3
 dpkg-buildpackage: info: source distribution unstable
@@ -1889,33 +1923,33 @@
 1..29
 ok 1 - use Bio::AlignIO;
 ok 2 - An object of class 'Bio::SimpleAlign' isa 'Bio::AnnotatableI'
-ok 3 - input filehandle method test : msf
-ok 4 - input filehandle method test : prodom
-ok 5 - input filehandle method test : xmfa
-ok 6 - input filehandle method test : po
-ok 7 - input filehandle method test : mase
-ok 8 - input filehandle method test : stockholm
-ok 9 - input filehandle method test : nexus
-ok 10 - input filehandle method test : clustalw
-ok 11 - input filehandle method test : selex
-ok 12 - input filehandle method test : fasta
-ok 13 - input filehandle method test : metafasta
-ok 14 - input filehandle method test : psi
-ok 15 - input filehandle method test : phylip
-ok 16 - input filehandle method test : pfam
-ok 17 - input filehandle method test : arp
+ok 3 - input filehandle method test : mase
+ok 4 - input filehandle method test : msf
+ok 5 - input filehandle method test : psi
+ok 6 - input filehandle method test : stockholm
+ok 7 - input filehandle method test : pfam
+ok 8 - input filehandle method test : selex
+ok 9 - input filehandle method test : phylip
+ok 10 - input filehandle method test : xmfa
+ok 11 - input filehandle method test : arp
+ok 12 - input filehandle method test : nexus
+ok 13 - input filehandle method test : prodom
+ok 14 - input filehandle method test : clustalw
+ok 15 - input filehandle method test : po
+ok 16 - input filehandle method test : metafasta
+ok 17 - input filehandle method test : fasta
 ok 18 - filehandle output test : msf
-ok 19 - filehandle output test : xmfa
-ok 20 - filehandle output test : po
-ok 21 - filehandle output test : stockholm
-ok 22 - filehandle output test : nexus
-ok 23 - filehandle output test : clustalw
-ok 24 - filehandle output test : selex
-ok 25 - filehandle output test : fasta
-ok 26 - filehandle output test : metafasta
-ok 27 - filehandle output test : psi
-ok 28 - filehandle output test : phylip
-ok 29 - filehandle output test : pfam
+ok 19 - filehandle output test : psi
+ok 20 - filehandle output test : stockholm
+ok 21 - filehandle output test : pfam
+ok 22 - filehandle output test : selex
+ok 23 - filehandle output test : phylip
+ok 24 - filehandle output test : xmfa
+ok 25 - filehandle output test : nexus
+ok 26 - filehandle output test : clustalw
+ok 27 - filehandle output test : po
+ok 28 - filehandle output test : metafasta
+ok 29 - filehandle output test : fasta
 ok
 t/AlignIO/arp.t ........................ 
 1..48
@@ -2853,8 +2887,8 @@
 ok 207 - 74.7485808732225
 ok 208 - large cross-contig spectrum
 ok 209
-ok 210 - 88.8076923076923
-ok 211 - 88.8076923076923
+ok 210 - 88.7692307692308
+ok 211 - 88.7692307692308
 ok 212
 ok 213
 ok 214
@@ -6054,23 +6088,23 @@
 ok 17 - to_string looks reasonable
 ok 18 - There are 8 root InterPro terms
 ok 19 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 20 - term Kringle in ontology InterPro
+ok 20 - term Binding Site in ontology InterPro
 ok 21 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 22 - term Binding Site in ontology InterPro
+ok 22 - term Cdc20/Fizzy in ontology InterPro
 ok 23 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 24 - term Region in ontology InterPro
+ok 24 - term Repeat in ontology InterPro
 ok 25 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 26 - term Cdc20/Fizzy in ontology InterPro
+ok 26 - term post-translational modification in ontology InterPro
 ok 27 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 28 - term Helix-turn-helix, AraC type  in ontology InterPro
+ok 28 - term Conserved Site in ontology InterPro
 ok 29 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
 ok 30 - term Integrins alpha chain in ontology InterPro
 ok 31 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 32 - term post-translational modification in ontology InterPro
+ok 32 - term Kringle in ontology InterPro
 ok 33 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 34 - term Conserved Site in ontology InterPro
+ok 34 - term Helix-turn-helix, AraC type  in ontology InterPro
 ok 35 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
-ok 36 - term Repeat in ontology InterPro
+ok 36 - term Region in ontology InterPro
 ok 37 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
 ok 38 - term Active Site in ontology InterPro
 ok 39 - An object of class 'Bio::Ontology::Ontology' isa 'Bio::Ontology::Ontology'
@@ -6095,14 +6129,14 @@
 ok 58
 ok 59
 ok 60
-ok 61 - Kringle term has one parent
-ok 62 - Kringle term has one ancestor
-ok 63 - Cdc20/Fizzy term has one parent
-ok 64 - Cdc20/Fizzy term has one ancestor
-ok 65 - Helix-turn-helix, AraC type  term has one parent
-ok 66 - Helix-turn-helix, AraC type  term has one ancestor
-ok 67 - Integrins alpha chain term has one parent
-ok 68 - Integrins alpha chain term has one ancestor
+ok 61 - Cdc20/Fizzy term has one parent
+ok 62 - Cdc20/Fizzy term has one ancestor
+ok 63 - Integrins alpha chain term has one parent
+ok 64 - Integrins alpha chain term has one ancestor
+ok 65 - Kringle term has one parent
+ok 66 - Kringle term has one ancestor
+ok 67 - Helix-turn-helix, AraC type  term has one parent
+ok 68 - Helix-turn-helix, AraC type  term has one ancestor
 ok 69 - secondary accession map has 2 keys
 ok
 t/Ontology/IO/obo.t .................... 
@@ -9234,24 +9268,24 @@
 t/SearchIO/SearchIO.t .................. 
 1..19
 ok 1 - use Bio::SearchIO;
-ok 2 - blast for fast.bls
-ok 3 - exonerate for f.exon
-ok 4 - fasta for f.psearch
-ok 5 - blast for filename.blast
-ok 6 - fasta for f.m9
-ok 7 - blast for f.blx
-ok 8 - blast for f.tblx
-ok 9 - fasta for f.fasta
-ok 10 - fasta for f.SSEARCH.m9
-ok 11 - fasta for f.fx
-ok 12 - exonerate for f.exonerate
-ok 13 - fasta for f.fy
-ok 14 - blastxml for f.xml
-ok 15 - fasta for f.ssearch
-ok 16 - fasta for f.osearch
-ok 17 - fasta for f.fa
-ok 18 - blastxml for f.blastxml
-ok 19 - blast for filename.bls
+ok 2 - fasta for f.fa
+ok 3 - blast for f.blx
+ok 4 - fasta for f.fy
+ok 5 - blast for f.tblx
+ok 6 - exonerate for f.exonerate
+ok 7 - fasta for f.SSEARCH.m9
+ok 8 - blast for filename.bls
+ok 9 - fasta for f.m9
+ok 10 - blastxml for f.xml
+ok 11 - blast for fast.bls
+ok 12 - fasta for f.psearch
+ok 13 - fasta for f.fasta
+ok 14 - blastxml for f.blastxml
+ok 15 - fasta for f.fx
+ok 16 - fasta for f.ssearch
+ok 17 - exonerate for f.exon
+ok 18 - fasta for f.osearch
+ok 19 - blast for filename.blast
 ok
 t/SearchIO/SimilarityPair.t ............ 
 1..12
@@ -10182,14 +10216,14 @@
 ok 910 - h cn: exact (0.92885) <= max (0.92885)
 ok 911 - bl2seq.blastx.out
 ok 912 - tile bl2seq.blastx.out hit 1 \#hsps 6
-ok 913 - q id: est (0.35714) = fast (0.35714)
-ok 914 - q cn: est (0.57143) = fast (0.57143)
+ok 913 - q id: est (0.71429) = fast (0.71429)
+ok 914 - q cn: est (1.00000) = fast (1.00000)
 ok 915 - q id: exact (0.70536) ~ est (0.70495)
 ok 916 - q id: exact (0.70536) <= max (0.94286)
 ok 917 - q cn: exact (0.78810) ~ est (0.78803)
 ok 918 - q cn: exact (0.78810) <= max (0.96429)
-ok 919 - q id: est (0.71429) = fast (0.71429)
-ok 920 - q cn: est (1.00000) = fast (1.00000)
+ok 919 - q id: est (0.35714) = fast (0.35714)
+ok 920 - q cn: est (0.57143) = fast (0.57143)
 ok 921 - h id: exact (0.61923) ~ est (0.61955)
 ok 922 - h id: exact (0.61923) <= max (0.64231)
 ok 923 - h cn: exact (0.73077) ~ est (0.73077)
@@ -10271,10 +10305,10 @@
 ok 999 - q id: exact (0.40541) <= max (0.40541)
 ok 1000 - q cn: exact (0.56757) ~ est (0.56757)
 ok 1001 - q cn: exact (0.56757) <= max (0.56757)
-ok 1002 - h id: est (0.36364) = fast (0.36364)
-ok 1003 - h cn: est (0.63636) = fast (0.63636)
-ok 1004 - h id: est (0.42308) = fast (0.42308)
-ok 1005 - h cn: est (0.53846) = fast (0.53846)
+ok 1002 - h id: est (0.42308) = fast (0.42308)
+ok 1003 - h cn: est (0.53846) = fast (0.53846)
+ok 1004 - h id: est (0.36364) = fast (0.36364)
+ok 1005 - h cn: est (0.63636) = fast (0.63636)
 ok 1006 - tile HUMBETGLOA.tblastx hit 10 \#hsps 1
 ok 1007 - q id: est (0.29167) = fast (0.29167)
 ok 1008 - q cn: est (0.39583) = fast (0.39583)
@@ -10344,12 +10378,12 @@
 ok 1072 - q cn: exact (0.58494) <= max (0.62179)
 ok 1073 - q id: est (0.37500) = fast (0.37500)
 ok 1074 - q cn: est (0.62500) = fast (0.62500)
-ok 1075 - h id: est (0.25352) = fast (0.25352)
-ok 1076 - h cn: est (0.47887) = fast (0.47887)
-ok 1077 - h id: exact (0.44118) ~ est (0.44118)
-ok 1078 - h id: exact (0.44118) <= max (0.44118)
-ok 1079 - h cn: exact (0.54412) ~ est (0.54412)
-ok 1080 - h cn: exact (0.54412) <= max (0.54412)
+ok 1075 - h id: exact (0.44118) ~ est (0.44118)
+ok 1076 - h id: exact (0.44118) <= max (0.44118)
+ok 1077 - h cn: exact (0.54412) ~ est (0.54412)
+ok 1078 - h cn: exact (0.54412) <= max (0.54412)
+ok 1079 - h id: est (0.25352) = fast (0.25352)
+ok 1080 - h cn: est (0.47887) = fast (0.47887)
 ok 1081 - h id: exact (0.39848) ~ est (0.40304)
 ok 1082 - h id: exact (0.39848) <= max (0.40355)
 ok 1083 - h cn: exact (0.58376) ~ est (0.58889)
@@ -11577,24 +11611,24 @@
 ok 1080
 ok 1081
 ok 1082
-ok 1083 - fasta for f.fasta
-ok 1084 - fasta for f.fy
-ok 1085 - fasta for f.fx
-ok 1086 - fasta for f.osearch
-ok 1087 - fasta for f.SSEARCH.m9
-ok 1088 - exonerate for f.exonerate
-ok 1089 - blast for filename.bls
-ok 1090 - blastxml for f.xml
-ok 1091 - blastxml for f.blastxml
+ok 1083 - blast for f.blx
+ok 1084 - exonerate for f.exonerate
+ok 1085 - blastxml for f.blastxml
+ok 1086 - blast for f.tblx
+ok 1087 - fasta for f.osearch
+ok 1088 - blastxml for f.xml
+ok 1089 - fasta for f.SSEARCH.m9
+ok 1090 - blast for filename.bls
+ok 1091 - fasta for f.fy
 ok 1092 - blast for fast.bls
-ok 1093 - blast for f.tblx
-ok 1094 - fasta for f.psearch
-ok 1095 - blast for filename.blast
-ok 1096 - exonerate for f.exon
-ok 1097 - fasta for f.m9
-ok 1098 - fasta for f.ssearch
-ok 1099 - blast for f.blx
-ok 1100 - fasta for f.fa
+ok 1093 - fasta for f.m9
+ok 1094 - fasta for f.ssearch
+ok 1095 - fasta for f.fx
+ok 1096 - fasta for f.fa
+ok 1097 - exonerate for f.exon
+ok 1098 - fasta for f.fasta
+ok 1099 - blast for filename.blast
+ok 1100 - fasta for f.psearch
 ok 1101
 ok 1102
 ok 1103
@@ -15087,7 +15121,7 @@
 ok 19
 not ok 20 # TODO Need to fix columns before start of seq w/ start > 1
 #   Failed (TODO) test at t/Seq/LocatableSeq.t line 47.
-#          got: 'Bio::Location::Simple=HASH(0x56495e6ca5b8)'
+#          got: 'Bio::Location::Simple=HASH(0x55851f52fb10)'
 #     expected: undef
 ok 21
 ok 22 - An object of class 'Bio::AlignIO::pfam' isa 'Bio::AlignIO'
@@ -16839,7 +16873,7 @@
 1..325
 ok 1 - use Bio::Factory::FTLocationFactory;
 ok 2 - An object of class 'Bio::Factory::FTLocationFactory' isa 'Bio::Factory::LocationFactoryI'
-ok 3 - Bio::Location::Fuzzy
+ok 3 - Bio::Location::Simple
 ok 4
 ok 5
 ok 6
@@ -16848,9 +16882,9 @@
 ok 9
 ok 10
 ok 11
-ok 12 - Location String: (23.45)..600
+ok 12 - Location String: 123^124
 ok 13
-ok 14 - Bio::Location::Split
+ok 14 - Bio::Location::Simple
 ok 15
 ok 16
 ok 17
@@ -16859,9 +16893,9 @@
 ok 20
 ok 21
 ok 22
-ok 23 - Location String: join(1..100,J00194.1:100..202)
+ok 23 - Location String: J00194:100..202
 ok 24
-ok 25 - Bio::Location::Fuzzy
+ok 25 - Bio::Location::Split
 ok 26
 ok 27
 ok 28
@@ -16870,7 +16904,7 @@
 ok 31
 ok 32
 ok 33
-ok 34 - Location String: (102.110)
+ok 34 - Location String: join(12..78,134..202)
 ok 35
 ok 36 - Bio::Location::Fuzzy
 ok 37
@@ -16881,7 +16915,7 @@
 ok 42
 ok 43
 ok 44
-ok 45 - Location String: <1..888
+ok 45 - Location String: ?..?
 ok 46
 ok 47 - Bio::Location::Fuzzy
 ok 48
@@ -16892,9 +16926,9 @@
 ok 53
 ok 54
 ok 55
-ok 56 - Location String: ?..>393
+ok 56 - Location String: complement(34..(122.126))
 ok 57
-ok 58 - Bio::Location::Simple
+ok 58 - Bio::Location::Fuzzy
 ok 59
 ok 60
 ok 61
@@ -16903,7 +16937,7 @@
 ok 64
 ok 65
 ok 66
-ok 67 - Location String: 123^124
+ok 67 - Location String: 1..?
 ok 68
 ok 69 - Bio::Location::Fuzzy
 ok 70
@@ -16914,9 +16948,9 @@
 ok 75
 ok 76
 ok 77
-ok 78 - Location String: ?1..12
+ok 78 - Location String: (23.45)..600
 ok 79
-ok 80 - Bio::Location::Fuzzy
+ok 80 - Bio::Location::Split
 ok 81
 ok 82
 ok 83
@@ -16925,9 +16959,9 @@
 ok 86
 ok 87
 ok 88
-ok 89 - Location String: <345..500
+ok 89 - Location String: complement(join(2691..4571,4918..5163))
 ok 90
-ok 91 - Bio::Location::Fuzzy
+ok 91 - Bio::Location::Split
 ok 92
 ok 93
 ok 94
@@ -16936,9 +16970,9 @@
 ok 97
 ok 98
 ok 99
-ok 100 - Location String: ?2465..2774
+ok 100 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
 ok 101
-ok 102 - Bio::Location::Simple
+ok 102 - Bio::Location::Fuzzy
 ok 103
 ok 104
 ok 105
@@ -16947,9 +16981,9 @@
 ok 108
 ok 109
 ok 110
-ok 111 - Location String: J00194:100..202
+ok 111 - Location String: <345..500
 ok 112
-ok 113 - Bio::Location::Split
+ok 113 - Bio::Location::Fuzzy
 ok 114
 ok 115
 ok 116
@@ -16958,7 +16992,7 @@
 ok 119
 ok 120
 ok 121
-ok 122 - Location String: join(12..78,134..202)
+ok 122 - Location String: ?..536
 ok 123
 ok 124 - Bio::Location::Fuzzy
 ok 125
@@ -16969,7 +17003,7 @@
 ok 130
 ok 131
 ok 132
-ok 133 - Location String: (122.133)..(204.221)
+ok 133 - Location String: 22..?64
 ok 134
 ok 135 - Bio::Location::Fuzzy
 ok 136
@@ -16980,9 +17014,9 @@
 ok 141
 ok 142
 ok 143
-ok 144 - Location String: (122.133)..(204.221)
+ok 144 - Location String: 1..>888
 ok 145
-ok 146 - Bio::Location::Fuzzy
+ok 146 - Bio::Location::Simple
 ok 147
 ok 148
 ok 149
@@ -16991,7 +17025,7 @@
 ok 152
 ok 153
 ok 154
-ok 155 - Location String: 145^177
+ok 155 - Location String: J00194:100..202
 ok 156
 ok 157 - Bio::Location::Fuzzy
 ok 158
@@ -17002,7 +17036,7 @@
 ok 163
 ok 164
 ok 165
-ok 166 - Location String: 1..?
+ok 166 - Location String: <1..888
 ok 167
 ok 168 - Bio::Location::Fuzzy
 ok 169
@@ -17013,7 +17047,7 @@
 ok 174
 ok 175
 ok 176
-ok 177 - Location String: 1..>888
+ok 177 - Location String: (102.110)
 ok 178
 ok 179 - Bio::Location::Fuzzy
 ok 180
@@ -17024,9 +17058,9 @@
 ok 185
 ok 186
 ok 187
-ok 188 - Location String: ?22..?64
+ok 188 - Location String: ?..>393
 ok 189
-ok 190 - Bio::Location::Fuzzy
+ok 190 - Bio::Location::Split
 ok 191
 ok 192
 ok 193
@@ -17035,9 +17069,9 @@
 ok 196
 ok 197
 ok 198
-ok 199 - Location String: complement(34..(122.126))
+ok 199 - Location String: join(1..100,J00194.1:100..202)
 ok 200
-ok 201 - Bio::Location::Split
+ok 201 - Bio::Location::Simple
 ok 202
 ok 203
 ok 204
@@ -17046,7 +17080,7 @@
 ok 207
 ok 208
 ok 209
-ok 210 - Location String: complement(join(2691..4571,4918..5163))
+ok 210 - Location String: 340..565
 ok 211
 ok 212 - Bio::Location::Fuzzy
 ok 213
@@ -17057,7 +17091,7 @@
 ok 218
 ok 219
 ok 220
-ok 221 - Location String: ?..?
+ok 221 - Location String: 145^177
 ok 222
 ok 223 - Bio::Location::Split
 ok 224
@@ -17068,9 +17102,9 @@
 ok 229
 ok 230
 ok 231
-ok 232 - Location String: join(AY016290.1:108..185,AY016291.1:1546..1599)
+ok 232 - Location String: complement(join(94468..94578,94578..>94889))
 ok 233
-ok 234 - Bio::Location::Simple
+ok 234 - Bio::Location::Fuzzy
 ok 235
 ok 236
 ok 237
@@ -17079,9 +17113,9 @@
 ok 240
 ok 241
 ok 242
-ok 243 - Location String: J00194:100..202
+ok 243 - Location String: ?2465..2774
 ok 244
-ok 245 - Bio::Location::Fuzzy
+ok 245 - Bio::Location::Simple
 ok 246
 ok 247
 ok 248
@@ -17090,7 +17124,7 @@
 ok 251
 ok 252
 ok 253
-ok 254 - Location String: ?..536
+ok 254 - Location String: 467
 ok 255
 ok 256 - Bio::Location::Fuzzy
 ok 257
@@ -17101,9 +17135,9 @@
 ok 262
 ok 263
 ok 264
-ok 265 - Location String: 22..?64
+ok 265 - Location String: ?22..?64
 ok 266
-ok 267 - Bio::Location::Split
+ok 267 - Bio::Location::Fuzzy
 ok 268
 ok 269
 ok 270
@@ -17112,7 +17146,7 @@
 ok 273
 ok 274
 ok 275
-ok 276 - Location String: complement(join(94468..94578,94578..>94889))
+ok 276 - Location String: (122.133)..(204.221)
 ok 277
 ok 278 - Bio::Location::Fuzzy
 ok 279
@@ -17123,9 +17157,9 @@
 ok 284
 ok 285
 ok 286
-ok 287 - Location String: <1..?
+ok 287 - Location String: (122.133)..(204.221)
 ok 288
-ok 289 - Bio::Location::Simple
+ok 289 - Bio::Location::Fuzzy
 ok 290
 ok 291
 ok 292
@@ -17134,9 +17168,9 @@
 ok 295
 ok 296
 ok 297
-ok 298 - Location String: 340..565
+ok 298 - Location String: ?1..12
 ok 299
-ok 300 - Bio::Location::Simple
+ok 300 - Bio::Location::Fuzzy
 ok 301
 ok 302
 ok 303
@@ -17145,7 +17179,7 @@
 ok 306
 ok 307
 ok 308
-ok 309 - Location String: 467
+ok 309 - Location String: <1..?
 ok 310
 ok 311 - complement(join(2691..4571,4918..5163))
 ok 312 - join(complement(4918..5163),complement(2691..4571))
@@ -18689,8 +18723,8 @@
 ok 266
 ok 267 - correct number of loops for T10
 ok 268 - correct number of loops for T11a
-ok 269
-ok 270 - correct number of loops for T11a
+ok 269 - correct number of loops for T11a
+ok 270
 ok 271 - correct number of loops for T11a
 ok 272 - correct number of loops for T11
 ok 273 - correct number of loops for T15
@@ -18748,8 +18782,8 @@
 ok 325
 ok 326
 ok 327 - correct number of loops for T10
-ok 328
-ok 329 - correct number of loops for T11a
+ok 328 - correct number of loops for T11a
+ok 329
 ok 330 - correct number of loops for T11a
 ok 331 - correct number of loops for T11a
 ok 332 - correct number of loops for T11
@@ -19784,8 +19818,8 @@
 ok 1361 - correct number of loops for T10
 ok 1362 - correct number of loops for T11a
 ok 1363 - correct number of loops for T11a
-ok 1364
-ok 1365 - correct number of loops for T11a
+ok 1364 - correct number of loops for T11a
+ok 1365
 ok 1366 - correct number of loops for T11a
 ok 1367 - correct number of loops for T11
 ok 1368
@@ -19810,8 +19844,8 @@
 ok 1387
 ok 1388 - correct number of loops for T10
 ok 1389 - correct number of loops for T11a
-ok 1390 - correct number of loops for T11a
-ok 1391
+ok 1390
+ok 1391 - correct number of loops for T11a
 ok 1392 - correct number of loops for T11a
 ok 1393 - correct number of loops for T11a
 ok 1394 - correct number of loops for T11
@@ -20102,7 +20136,7 @@
 not ok 9 - primary_id # TODO possible bug: RichSeq not setting primary_id?
 #   Failed (TODO) test 'primary_id'
 #   at t/SeqIO/gcg.t line 54.
-#          got: 'Bio::PrimarySeq=HASH(0x55fc4c110108)'
+#          got: 'Bio::PrimarySeq=HASH(0x5568c276b060)'
 #     expected: 'roa1_drome'
 ok 10 - description
 ok 11
@@ -20529,21 +20563,21 @@
 ok 2 - Bio::SeqIO::mbsout is at least api version 1.1.3
 ok 3 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout'
 ok 4 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout'
-ok 5 - Get POP_RECOMB_PARAM_PER_SITE
-ok 6 - Get NREPS
-ok 7 - Get NEXT_RUN_NUM
-ok 8 - Get RUNS
+ok 5 - Get NREPS
+ok 6 - Get CURRENT_RUN_SEGSITES
+ok 7 - Get SEGSITES
+ok 8 - Get TRAJ_FILENAME
 ok 9 - Get LAST_READ_HAP_NUM
-ok 10 - Get TRAJ_FILENAME
-ok 11 - Get POP_MUT_PARAM_PER_SITE
-ok 12 - Get NFILES
-ok 13 - Get MBS_INFO_LINE
-ok 14 - Get SELPOS
+ok 10 - Get NFILES
+ok 11 - Get SELPOS
+ok 12 - Get MBS_INFO_LINE
+ok 13 - Get RUNS
+ok 14 - Get POP_RECOMB_PARAM_PER_SITE
 ok 15 - Get POSITIONS
-ok 16 - Get CURRENT_RUN_SEGSITES
-ok 17 - Get TOT_RUN_HAPS
-ok 18 - Get SEGSITES
-ok 19 - Get NSITES
+ok 16 - Get TOT_RUN_HAPS
+ok 17 - Get POP_MUT_PARAM_PER_SITE
+ok 18 - Get NSITES
+ok 19 - Get NEXT_RUN_NUM
 ok 20 - Get next_hap at beginning of run
 ok 21 - Get next_hap after beginning of run
 ok 22 - Get next_pop after beginning of pop
@@ -20554,21 +20588,21 @@
 ok 27 - Get next_run at beginning of run
 ok 28 - have all lines been read?
 ok 29 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout'
-ok 30 - Get CURRENT_RUN_SEGSITES
-ok 31 - Get TOT_RUN_HAPS
-ok 32 - Get SEGSITES
-ok 33 - Get NSITES
-ok 34 - Get NFILES
-ok 35 - Get MBS_INFO_LINE
-ok 36 - Get POSITIONS
+ok 30 - Get NEXT_RUN_NUM
+ok 31 - Get NSITES
+ok 32 - Get POP_MUT_PARAM_PER_SITE
+ok 33 - Get TOT_RUN_HAPS
+ok 34 - Get POP_RECOMB_PARAM_PER_SITE
+ok 35 - Get POSITIONS
+ok 36 - Get MBS_INFO_LINE
 ok 37 - Get SELPOS
-ok 38 - Get NREPS
-ok 39 - Get NEXT_RUN_NUM
-ok 40 - Get RUNS
-ok 41 - Get LAST_READ_HAP_NUM
-ok 42 - Get TRAJ_FILENAME
-ok 43 - Get POP_MUT_PARAM_PER_SITE
-ok 44 - Get POP_RECOMB_PARAM_PER_SITE
+ok 38 - Get RUNS
+ok 39 - Get NFILES
+ok 40 - Get LAST_READ_HAP_NUM
+ok 41 - Get TRAJ_FILENAME
+ok 42 - Get SEGSITES
+ok 43 - Get CURRENT_RUN_SEGSITES
+ok 44 - Get NREPS
 ok 45 - Get next_hap at beginning of run
 ok 46 - Get next_hap after beginning of run
 ok 47 - Testing mbsout::outgroup
@@ -20579,21 +20613,21 @@
 ok 52 - Get next_run after hap
 ok 53 - next run should be 5.
 ok 54 - An object of class 'Bio::SeqIO::mbsout' isa 'Bio::SeqIO::mbsout'
-ok 55 - Get POP_RECOMB_PARAM_PER_SITE
-ok 56 - Get POP_MUT_PARAM_PER_SITE
-ok 57 - Get RUNS
-ok 58 - Get LAST_READ_HAP_NUM
-ok 59 - Get TRAJ_FILENAME
-ok 60 - Get NREPS
-ok 61 - Get NEXT_RUN_NUM
-ok 62 - Get POSITIONS
-ok 63 - Get SELPOS
-ok 64 - Get NFILES
-ok 65 - Get MBS_INFO_LINE
-ok 66 - Get SEGSITES
-ok 67 - Get NSITES
-ok 68 - Get CURRENT_RUN_SEGSITES
-ok 69 - Get TOT_RUN_HAPS
+ok 55 - Get POP_MUT_PARAM_PER_SITE
+ok 56 - Get TOT_RUN_HAPS
+ok 57 - Get POSITIONS
+ok 58 - Get POP_RECOMB_PARAM_PER_SITE
+ok 59 - Get NEXT_RUN_NUM
+ok 60 - Get NSITES
+ok 61 - Get TRAJ_FILENAME
+ok 62 - Get LAST_READ_HAP_NUM
+ok 63 - Get SEGSITES
+ok 64 - Get CURRENT_RUN_SEGSITES
+ok 65 - Get NREPS
+ok 66 - Get RUNS
+ok 67 - Get MBS_INFO_LINE
+ok 68 - Get SELPOS
+ok 69 - Get NFILES
 ok 70 - Get next_run at end/beginning of run
 ok 71 - have all lines been read?
 ok 72 - Get next_run at eof
@@ -20615,16 +20649,16 @@
 ok 2 - Bio::SeqIO::msout is at least api version 1.1.5
 ok 3 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
 ok 4 - Get MS_INFO_LINE
-ok 5 - Get RUNS
-ok 6 - Get LAST_READ_HAP_NUM
-ok 7 - Get TOT_RUN_HAPS
-ok 8 - Get CURRENT_RUN_SEGSITES
-ok 9 - Get POSITIONS
-ok 10 - Get SEEDS
-ok 11 - Get SEGSITES
-ok 12 - Get N_SITES
-ok 13 - Get POPS
-ok 14 - Get NEXT_RUN_NUM
+ok 5 - Get TOT_RUN_HAPS
+ok 6 - Get SEGSITES
+ok 7 - Get CURRENT_RUN_SEGSITES
+ok 8 - Get SEEDS
+ok 9 - Get NEXT_RUN_NUM
+ok 10 - Get LAST_READ_HAP_NUM
+ok 11 - Get RUNS
+ok 12 - Get POPS
+ok 13 - Get N_SITES
+ok 14 - Get POSITIONS
 ok 15 - Get next_hap at beginning of run
 ok 16 - Get next_hap after beginning of run
 ok 17 - Testing msout::outgroup
@@ -20637,17 +20671,17 @@
 ok 24 - Get next_run at beginning of run
 ok 25 - have all lines been read?
 ok 26 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
-ok 27 - Get NEXT_RUN_NUM
-ok 28 - Get N_SITES
-ok 29 - Get POPS
-ok 30 - Get SEGSITES
-ok 31 - Get POSITIONS
-ok 32 - Get SEEDS
-ok 33 - Get CURRENT_RUN_SEGSITES
-ok 34 - Get TOT_RUN_HAPS
-ok 35 - Get MS_INFO_LINE
-ok 36 - Get RUNS
-ok 37 - Get LAST_READ_HAP_NUM
+ok 27 - Get CURRENT_RUN_SEGSITES
+ok 28 - Get TOT_RUN_HAPS
+ok 29 - Get SEGSITES
+ok 30 - Get MS_INFO_LINE
+ok 31 - Get RUNS
+ok 32 - Get LAST_READ_HAP_NUM
+ok 33 - Get NEXT_RUN_NUM
+ok 34 - Get SEEDS
+ok 35 - Get POPS
+ok 36 - Get N_SITES
+ok 37 - Get POSITIONS
 ok 38 - Get next_hap at beginning of run
 ok 39 - Get next_hap after beginning of run
 ok 40 - Testing msout::outgroup
@@ -20659,16 +20693,16 @@
 ok 46 - next run should be 5.
 ok 47 - Get last hap through next_hap
 ok 48 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
-ok 49 - Get CURRENT_RUN_SEGSITES
+ok 49 - Get POSITIONS
 ok 50 - Get POPS
-ok 51 - Get NEXT_RUN_NUM
-ok 52 - Get SEEDS
-ok 53 - Get LAST_READ_HAP_NUM
-ok 54 - Get RUNS
-ok 55 - Get POSITIONS
+ok 51 - Get LAST_READ_HAP_NUM
+ok 52 - Get RUNS
+ok 53 - Get SEEDS
+ok 54 - Get NEXT_RUN_NUM
+ok 55 - Get CURRENT_RUN_SEGSITES
 ok 56 - Get MS_INFO_LINE
-ok 57 - Get TOT_RUN_HAPS
-ok 58 - Get SEGSITES
+ok 57 - Get SEGSITES
+ok 58 - Get TOT_RUN_HAPS
 ok 59 - Get next_pop at end of run
 ok 60 - have all lines been read?
 ok 61 - Get next_pop at eof
@@ -20676,17 +20710,17 @@
 ok 63 - Get next_hap at eof
 ok 64 - Get next_seq at eof
 ok 65 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
-ok 66 - Get CURRENT_RUN_SEGSITES
-ok 67 - Get TOT_RUN_HAPS
-ok 68 - Get LAST_READ_HAP_NUM
-ok 69 - Get MS_INFO_LINE
-ok 70 - Get RUNS
-ok 71 - Get NEXT_RUN_NUM
-ok 72 - Get POPS
-ok 73 - Get N_SITES
-ok 74 - Get SEGSITES
-ok 75 - Get SEEDS
-ok 76 - Get POSITIONS
+ok 66 - Get N_SITES
+ok 67 - Get POPS
+ok 68 - Get POSITIONS
+ok 69 - Get SEGSITES
+ok 70 - Get TOT_RUN_HAPS
+ok 71 - Get MS_INFO_LINE
+ok 72 - Get CURRENT_RUN_SEGSITES
+ok 73 - Get NEXT_RUN_NUM
+ok 74 - Get SEEDS
+ok 75 - Get RUNS
+ok 76 - Get LAST_READ_HAP_NUM
 ok 77 - Get next_hap at beginning of run
 ok 78 - Get next_hap after beginning of run
 ok 79 - Testing msout::outgroup
@@ -20703,16 +20737,16 @@
 ok 90 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
 ok 91 - Caught error in bad msout file 2
 ok 92 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
-ok 93 - Get SEGSITES
-ok 94 - Get POSITIONS
-ok 95 - Get SEEDS
+ok 93 - Get POSITIONS
+ok 94 - Get POPS
+ok 95 - Get N_SITES
 ok 96 - Get NEXT_RUN_NUM
-ok 97 - Get N_SITES
-ok 98 - Get POPS
-ok 99 - Get TOT_RUN_HAPS
-ok 100 - Get RUNS
-ok 101 - Get MS_INFO_LINE
-ok 102 - Get LAST_READ_HAP_NUM
+ok 97 - Get SEEDS
+ok 98 - Get RUNS
+ok 99 - Get LAST_READ_HAP_NUM
+ok 100 - Get TOT_RUN_HAPS
+ok 101 - Get SEGSITES
+ok 102 - Get MS_INFO_LINE
 ok 103 - Get CURRENT_RUN_SEGSITES
 ok 104 - Get next_hap at beginning of run
 ok 105 - Get next_hap after beginning of run
@@ -20726,17 +20760,17 @@
 ok 113 - Get next_run at beginning of run
 ok 114 - have all lines been read?
 ok 115 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
-ok 116 - Get N_SITES
-ok 117 - Get POPS
-ok 118 - Get NEXT_RUN_NUM
-ok 119 - Get POSITIONS
-ok 120 - Get SEEDS
-ok 121 - Get SEGSITES
-ok 122 - Get CURRENT_RUN_SEGSITES
-ok 123 - Get RUNS
-ok 124 - Get MS_INFO_LINE
-ok 125 - Get LAST_READ_HAP_NUM
-ok 126 - Get TOT_RUN_HAPS
+ok 116 - Get CURRENT_RUN_SEGSITES
+ok 117 - Get MS_INFO_LINE
+ok 118 - Get SEGSITES
+ok 119 - Get TOT_RUN_HAPS
+ok 120 - Get LAST_READ_HAP_NUM
+ok 121 - Get RUNS
+ok 122 - Get SEEDS
+ok 123 - Get NEXT_RUN_NUM
+ok 124 - Get N_SITES
+ok 125 - Get POPS
+ok 126 - Get POSITIONS
 ok 127 - Get next_hap at beginning of run
 ok 128 - Get next_hap after beginning of run
 ok 129 - Testing msout::outgroup
@@ -20749,16 +20783,16 @@
 ok 136 - Get last hap through next_hap
 ok 137 - An object of class 'Bio::SeqIO::msout' isa 'Bio::SeqIO::msout'
 ok 138 - Get CURRENT_RUN_SEGSITES
-ok 139 - Get TOT_RUN_HAPS
-ok 140 - Get MS_INFO_LINE
-ok 141 - Get RUNS
+ok 139 - Get MS_INFO_LINE
+ok 140 - Get TOT_RUN_HAPS
+ok 141 - Get SEGSITES
 ok 142 - Get LAST_READ_HAP_NUM
-ok 143 - Get NEXT_RUN_NUM
-ok 144 - Get N_SITES
-ok 145 - Get POPS
-ok 146 - Get SEGSITES
-ok 147 - Get POSITIONS
-ok 148 - Get SEEDS
+ok 143 - Get RUNS
+ok 144 - Get NEXT_RUN_NUM
+ok 145 - Get SEEDS
+ok 146 - Get POPS
+ok 147 - Get N_SITES
+ok 148 - Get POSITIONS
 ok 149 - Get next_hap at beginning of run
 ok 150 - Get next_hap after beginning of run
 ok 151 - Testing msout::outgroup
@@ -20900,7 +20934,7 @@
 not ok 29 - accuracies # TODO documentation and code for accuracies() do not match
 #   Failed (TODO) test 'accuracies'
 #   at t/SeqIO/scf.t line 78.
-#          got: 'ARRAY(0x5577dcf872c8)'
+#          got: 'ARRAY(0x565306bf2ca8)'
 #     expected: '482'
 ok 30
 ok 31 - sub_peak_index
@@ -20989,9 +21023,9 @@
 ok 19 - dblink source
 ok 20 - dblink ID
 ok 21 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
-ok 22 - property with value
+ok 22 - boolean property
 ok 23 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
-ok 24 - boolean property
+ok 24 - property with value
 ok 25 - writer ok
 ok 26 - outfile is created
 ok 27 - seqXML version
@@ -21012,9 +21046,9 @@
 ok 42 - dblink source
 ok 43 - dblink ID
 ok 44 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
-ok 45 - property with value
+ok 45 - boolean property
 ok 46 - An object of class 'Bio::Annotation::SimpleValue' isa 'Bio::Annotation::SimpleValue'
-ok 47 - boolean property
+ok 47 - property with value
 ok 48 - outfile is created
 ok 49 - seqXML version
 ok 50 - source
@@ -25087,7 +25121,7 @@
 ok
 t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
 All tests successful.
-Files=325, Tests=22589, 154 wallclock secs ( 4.34 usr  1.08 sys + 136.92 cusr 15.42 csys = 157.76 CPU)
+Files=325, Tests=22589, 192 wallclock secs ( 4.48 usr  1.18 sys + 170.36 cusr 15.07 csys = 191.09 CPU)
 Result: PASS
    create-stamp debian/debhelper-build-stamp
  fakeroot debian/rules binary
@@ -26831,20 +26865,22 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'libbio-perl-perl' in '../libbio-perl-perl_1.7.2-3_all.deb'.
 dpkg-deb: building package 'bioperl' in '../bioperl_1.7.2-3_all.deb'.
+dpkg-deb: building package 'libbio-perl-perl' in '../libbio-perl-perl_1.7.2-3_all.deb'.
  dpkg-genbuildinfo --build=binary
  dpkg-genchanges --build=binary >../bioperl_1.7.2-3_amd64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
  dpkg-source --after-build .
 dpkg-buildpackage: info: binary-only upload (no source included)
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/41996/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/41996/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/11805 and its subdirectories
-I: Current time: Wed Aug 24 01:51:30 -12 2022
-I: pbuilder-time-stamp: 1661349090
+I: removing directory /srv/workspace/pbuilder/41996 and its subdirectories
+I: Current time: Thu Jul 22 21:33:12 +14 2021
+I: pbuilder-time-stamp: 1626939192