Diff of the two buildlogs:

--
--- b1/build.log	2023-04-30 05:09:46.986939296 +0000
+++ b2/build.log	2023-04-30 05:14:37.206200308 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Fri May 31 23:31:09 -12 2024
-I: pbuilder-time-stamp: 1717241469
+I: Current time: Sun Apr 30 19:09:49 +14 2023
+I: pbuilder-time-stamp: 1682831389
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
 I: copying local configuration
@@ -16,7 +16,7 @@
 I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz]
 I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz]
 I: Extracting source
-gpgv: Signature made Tue Sep  6 03:33:36 2022 -12
+gpgv: Signature made Wed Sep  7 05:33:36 2022 +14
 gpgv:                using RSA key 2D65BC1EB9665A6E97F9730AB3F5945285219E1F
 gpgv:                issuer "mdbilal@disroot.org"
 gpgv: Can't check signature: No public key
@@ -35,135 +35,167 @@
 dpkg-source: info: applying gcc11.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/621218/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos1-amd64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Apr 30 19:10 /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/1180282/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/1180282/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='bookworm'
-  HOME='/root'
-  HOST_ARCH='amd64'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
+  BASH_VERSION='5.2.15(1)-release'
+  BUILDDIR=/build
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=amd64
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
+  DIRSTACK=()
+  DISTRIBUTION=bookworm
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=x86_64
+  HOST_ARCH=amd64
   IFS=' 	
   '
-  INVOCATION_ID='2795b59eac434ee4b103dcc64cc4c0e1'
-  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='621218'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=580994be2149478f94ff6edc74d075c3
+  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=1180282
   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.6OIiMJTx/pbuilderrc_JMDA --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6OIiMJTx/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc'
-  SUDO_GID='110'
-  SUDO_UID='105'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://85.184.249.68:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.6OIiMJTx/pbuilderrc_RQFB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6OIiMJTx/b2 --logfile b2/build.log --extrapackages usrmerge tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc'
+  SUDO_GID=110
+  SUDO_UID=105
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://78.137.99.97:3128
 I: uname -a
-  Linux ionos5-amd64 6.1.0-0.deb11.6-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.15-1~bpo11+1 (2023-03-16) x86_64 GNU/Linux
+  Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux
 I: ls -l /bin
   total 5632
-  -rwxr-xr-x 1 root root 1265648 Apr 23  2023 bash
-  -rwxr-xr-x 3 root root   39224 Sep 18  2022 bunzip2
-  -rwxr-xr-x 3 root root   39224 Sep 18  2022 bzcat
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzcmp -> bzdiff
-  -rwxr-xr-x 1 root root    2225 Sep 18  2022 bzdiff
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzegrep -> bzgrep
-  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzfgrep -> bzgrep
-  -rwxr-xr-x 1 root root    3775 Sep 18  2022 bzgrep
-  -rwxr-xr-x 3 root root   39224 Sep 18  2022 bzip2
-  -rwxr-xr-x 1 root root   14568 Sep 18  2022 bzip2recover
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzless -> bzmore
-  -rwxr-xr-x 1 root root    1297 Sep 18  2022 bzmore
-  -rwxr-xr-x 1 root root   44016 Sep 20  2022 cat
-  -rwxr-xr-x 1 root root   68656 Sep 20  2022 chgrp
-  -rwxr-xr-x 1 root root   64496 Sep 20  2022 chmod
-  -rwxr-xr-x 1 root root   72752 Sep 20  2022 chown
-  -rwxr-xr-x 1 root root  151152 Sep 20  2022 cp
-  -rwxr-xr-x 1 root root  125640 Jan  5  2023 dash
-  -rwxr-xr-x 1 root root  121904 Sep 20  2022 date
-  -rwxr-xr-x 1 root root   89240 Sep 20  2022 dd
-  -rwxr-xr-x 1 root root  102200 Sep 20  2022 df
-  -rwxr-xr-x 1 root root  151344 Sep 20  2022 dir
-  -rwxr-xr-x 1 root root   88656 Mar 22  2023 dmesg
-  lrwxrwxrwx 1 root root       8 Dec 19  2022 dnsdomainname -> hostname
-  lrwxrwxrwx 1 root root       8 Dec 19  2022 domainname -> hostname
-  -rwxr-xr-x 1 root root   43856 Sep 20  2022 echo
-  -rwxr-xr-x 1 root root      41 Jan 24  2023 egrep
-  -rwxr-xr-x 1 root root   35664 Sep 20  2022 false
-  -rwxr-xr-x 1 root root      41 Jan 24  2023 fgrep
-  -rwxr-xr-x 1 root root   85600 Mar 22  2023 findmnt
-  -rwsr-xr-x 1 root root   35128 Mar 22  2023 fusermount
-  -rwxr-xr-x 1 root root  203152 Jan 24  2023 grep
-  -rwxr-xr-x 2 root root    2346 Apr  9  2022 gunzip
-  -rwxr-xr-x 1 root root    6447 Apr  9  2022 gzexe
-  -rwxr-xr-x 1 root root   98136 Apr  9  2022 gzip
-  -rwxr-xr-x 1 root root   22680 Dec 19  2022 hostname
-  -rwxr-xr-x 1 root root   72824 Sep 20  2022 ln
-  -rwxr-xr-x 1 root root   53024 Mar 23  2023 login
-  -rwxr-xr-x 1 root root  151344 Sep 20  2022 ls
-  -rwxr-xr-x 1 root root  207168 Mar 22  2023 lsblk
-  -rwxr-xr-x 1 root root   97552 Sep 20  2022 mkdir
-  -rwxr-xr-x 1 root root   72912 Sep 20  2022 mknod
-  -rwxr-xr-x 1 root root   43952 Sep 20  2022 mktemp
-  -rwxr-xr-x 1 root root   59712 Mar 22  2023 more
-  -rwsr-xr-x 1 root root   59704 Mar 22  2023 mount
-  -rwxr-xr-x 1 root root   18744 Mar 22  2023 mountpoint
-  -rwxr-xr-x 1 root root  142968 Sep 20  2022 mv
-  lrwxrwxrwx 1 root root       8 Dec 19  2022 nisdomainname -> hostname
-  lrwxrwxrwx 1 root root      14 Apr  2  2023 pidof -> /sbin/killall5
-  -rwxr-xr-x 1 root root   43952 Sep 20  2022 pwd
-  lrwxrwxrwx 1 root root       4 Apr 23  2023 rbash -> bash
-  -rwxr-xr-x 1 root root   52112 Sep 20  2022 readlink
-  -rwxr-xr-x 1 root root   72752 Sep 20  2022 rm
-  -rwxr-xr-x 1 root root   56240 Sep 20  2022 rmdir
-  -rwxr-xr-x 1 root root   27560 Nov  2  2022 run-parts
-  -rwxr-xr-x 1 root root  126424 Jan  5  2023 sed
-  lrwxrwxrwx 1 root root       4 Jan  5  2023 sh -> dash
-  -rwxr-xr-x 1 root root   43888 Sep 20  2022 sleep
-  -rwxr-xr-x 1 root root   85008 Sep 20  2022 stty
-  -rwsr-xr-x 1 root root   72000 Mar 22  2023 su
-  -rwxr-xr-x 1 root root   39824 Sep 20  2022 sync
-  -rwxr-xr-x 1 root root  531984 Apr  6  2023 tar
-  -rwxr-xr-x 1 root root   14520 Nov  2  2022 tempfile
-  -rwxr-xr-x 1 root root  109616 Sep 20  2022 touch
-  -rwxr-xr-x 1 root root   35664 Sep 20  2022 true
-  -rwxr-xr-x 1 root root   14568 Mar 22  2023 ulockmgr_server
-  -rwsr-xr-x 1 root root   35128 Mar 22  2023 umount
-  -rwxr-xr-x 1 root root   43888 Sep 20  2022 uname
-  -rwxr-xr-x 2 root root    2346 Apr  9  2022 uncompress
-  -rwxr-xr-x 1 root root  151344 Sep 20  2022 vdir
-  -rwxr-xr-x 1 root root   72024 Mar 22  2023 wdctl
-  lrwxrwxrwx 1 root root       8 Dec 19  2022 ypdomainname -> hostname
-  -rwxr-xr-x 1 root root    1984 Apr  9  2022 zcat
-  -rwxr-xr-x 1 root root    1678 Apr  9  2022 zcmp
-  -rwxr-xr-x 1 root root    6460 Apr  9  2022 zdiff
-  -rwxr-xr-x 1 root root      29 Apr  9  2022 zegrep
-  -rwxr-xr-x 1 root root      29 Apr  9  2022 zfgrep
-  -rwxr-xr-x 1 root root    2081 Apr  9  2022 zforce
-  -rwxr-xr-x 1 root root    8103 Apr  9  2022 zgrep
-  -rwxr-xr-x 1 root root    2206 Apr  9  2022 zless
-  -rwxr-xr-x 1 root root    1842 Apr  9  2022 zmore
-  -rwxr-xr-x 1 root root    4577 Apr  9  2022 znew
-I: user script /srv/workspace/pbuilder/621218/tmp/hooks/D02_print_environment finished
+  -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash
+  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bunzip2
+  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bzcat
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzcmp -> bzdiff
+  -rwxr-xr-x 1 root root    2225 Sep 19  2022 bzdiff
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzegrep -> bzgrep
+  -rwxr-xr-x 1 root root    4893 Nov 28  2021 bzexe
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzfgrep -> bzgrep
+  -rwxr-xr-x 1 root root    3775 Sep 19  2022 bzgrep
+  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bzip2
+  -rwxr-xr-x 1 root root   14568 Sep 19  2022 bzip2recover
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzless -> bzmore
+  -rwxr-xr-x 1 root root    1297 Sep 19  2022 bzmore
+  -rwxr-xr-x 1 root root   44016 Sep 21  2022 cat
+  -rwxr-xr-x 1 root root   68656 Sep 21  2022 chgrp
+  -rwxr-xr-x 1 root root   64496 Sep 21  2022 chmod
+  -rwxr-xr-x 1 root root   72752 Sep 21  2022 chown
+  -rwxr-xr-x 1 root root  151152 Sep 21  2022 cp
+  -rwxr-xr-x 1 root root  125640 Jan  6 03:20 dash
+  -rwxr-xr-x 1 root root  121904 Sep 21  2022 date
+  -rwxr-xr-x 1 root root   89240 Sep 21  2022 dd
+  -rwxr-xr-x 1 root root  102200 Sep 21  2022 df
+  -rwxr-xr-x 1 root root  151344 Sep 21  2022 dir
+  -rwxr-xr-x 1 root root   88656 Mar 24 00:02 dmesg
+  lrwxrwxrwx 1 root root       8 Dec 20 03:33 dnsdomainname -> hostname
+  lrwxrwxrwx 1 root root       8 Dec 20 03:33 domainname -> hostname
+  -rwxr-xr-x 1 root root   43856 Sep 21  2022 echo
+  -rwxr-xr-x 1 root root      41 Jan 25 04:43 egrep
+  -rwxr-xr-x 1 root root   35664 Sep 21  2022 false
+  -rwxr-xr-x 1 root root      41 Jan 25 04:43 fgrep
+  -rwxr-xr-x 1 root root   85600 Mar 24 00:02 findmnt
+  -rwsr-xr-x 1 root root   35128 Mar 23 22:35 fusermount
+  -rwxr-xr-x 1 root root  203152 Jan 25 04:43 grep
+  -rwxr-xr-x 2 root root    2346 Apr 10  2022 gunzip
+  -rwxr-xr-x 1 root root    6447 Apr 10  2022 gzexe
+  -rwxr-xr-x 1 root root   98136 Apr 10  2022 gzip
+  -rwxr-xr-x 1 root root   22680 Dec 20 03:33 hostname
+  -rwxr-xr-x 1 root root   72824 Sep 21  2022 ln
+  -rwxr-xr-x 1 root root   53024 Mar 24 02:40 login
+  -rwxr-xr-x 1 root root  151344 Sep 21  2022 ls
+  -rwxr-xr-x 1 root root  207168 Mar 24 00:02 lsblk
+  -rwxr-xr-x 1 root root   97552 Sep 21  2022 mkdir
+  -rwxr-xr-x 1 root root   72912 Sep 21  2022 mknod
+  -rwxr-xr-x 1 root root   43952 Sep 21  2022 mktemp
+  -rwxr-xr-x 1 root root   59712 Mar 24 00:02 more
+  -rwsr-xr-x 1 root root   59704 Mar 24 00:02 mount
+  -rwxr-xr-x 1 root root   18744 Mar 24 00:02 mountpoint
+  -rwxr-xr-x 1 root root  142968 Sep 21  2022 mv
+  lrwxrwxrwx 1 root root       8 Dec 20 03:33 nisdomainname -> hostname
+  lrwxrwxrwx 1 root root      14 Apr  3 20:25 pidof -> /sbin/killall5
+  -rwxr-xr-x 1 root root   43952 Sep 21  2022 pwd
+  lrwxrwxrwx 1 root root       4 Apr 24 11:23 rbash -> bash
+  -rwxr-xr-x 1 root root   52112 Sep 21  2022 readlink
+  -rwxr-xr-x 1 root root   72752 Sep 21  2022 rm
+  -rwxr-xr-x 1 root root   56240 Sep 21  2022 rmdir
+  -rwxr-xr-x 1 root root   27560 Nov  3 06:31 run-parts
+  -rwxr-xr-x 1 root root  126424 Jan  6 09:55 sed
+  lrwxrwxrwx 1 root root       9 Apr 30 19:10 sh -> /bin/bash
+  -rwxr-xr-x 1 root root   43888 Sep 21  2022 sleep
+  -rwxr-xr-x 1 root root   85008 Sep 21  2022 stty
+  -rwsr-xr-x 1 root root   72000 Mar 24 00:02 su
+  -rwxr-xr-x 1 root root   39824 Sep 21  2022 sync
+  -rwxr-xr-x 1 root root  531984 Apr  7 04:25 tar
+  -rwxr-xr-x 1 root root   14520 Nov  3 06:31 tempfile
+  -rwxr-xr-x 1 root root  109616 Sep 21  2022 touch
+  -rwxr-xr-x 1 root root   35664 Sep 21  2022 true
+  -rwxr-xr-x 1 root root   14568 Mar 23 22:35 ulockmgr_server
+  -rwsr-xr-x 1 root root   35128 Mar 24 00:02 umount
+  -rwxr-xr-x 1 root root   43888 Sep 21  2022 uname
+  -rwxr-xr-x 2 root root    2346 Apr 10  2022 uncompress
+  -rwxr-xr-x 1 root root  151344 Sep 21  2022 vdir
+  -rwxr-xr-x 1 root root   72024 Mar 24 00:02 wdctl
+  lrwxrwxrwx 1 root root       8 Dec 20 03:33 ypdomainname -> hostname
+  -rwxr-xr-x 1 root root    1984 Apr 10  2022 zcat
+  -rwxr-xr-x 1 root root    1678 Apr 10  2022 zcmp
+  -rwxr-xr-x 1 root root    6460 Apr 10  2022 zdiff
+  -rwxr-xr-x 1 root root      29 Apr 10  2022 zegrep
+  -rwxr-xr-x 1 root root      29 Apr 10  2022 zfgrep
+  -rwxr-xr-x 1 root root    2081 Apr 10  2022 zforce
+  -rwxr-xr-x 1 root root    8103 Apr 10  2022 zgrep
+  -rwxr-xr-x 1 root root    2206 Apr 10  2022 zless
+  -rwxr-xr-x 1 root root    1842 Apr 10  2022 zmore
+  -rwxr-xr-x 1 root root    4577 Apr 10  2022 znew
+I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -298,7 +330,7 @@
 Get: 85 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp-dev amd64 1.9.5-4 [26.4 kB]
 Get: 86 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB]
 Get: 87 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB]
-Fetched 61.0 MB in 1s (90.4 MB/s)
+Fetched 61.0 MB in 2s (30.2 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libproc2-0:amd64.
 (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 ... 19596 files and directories currently installed.)
@@ -665,8 +697,19 @@
 Writing extended state information...
 Building tag database...
  -> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+usrmerge is already the newest version (35).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 I: Building the package
-I: Running cd /build/tvc-5.0.3+git20151221.80e144e+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  > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes
+I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/A99_set_merged_usr starting
+Re-configuring usrmerge...
+removed '/etc/unsupported-skip-usrmerge-conversion'
+The system has been successfully converted.
+I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/tvc-5.0.3+git20151221.80e144e+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  > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes
 dpkg-buildpackage: info: source package tvc
 dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5
 dpkg-buildpackage: info: source distribution unstable
@@ -720,7 +763,7 @@
 
 -- Build files have been written to: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu
    dh_auto_build
-	cd obj-x86_64-linux-gnu && make -j16 "INSTALL=install --strip-program=true" VERBOSE=1
+	cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1
 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
 /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
 /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks
@@ -728,78 +771,98 @@
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+make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
+cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color=
 make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
 cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color=
+make  -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend
 make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
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-make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
-cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color=
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+make  -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build
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-[  9%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
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+[  4%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o
+/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp
+[  6%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o
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-[ 30%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o
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-[ 33%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o
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+/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
+  336 |         save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
+      |                                          ^~~~~~~~
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+/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
+/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
+  678 |         fread(buf, 1, 28, fp->file);
+      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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-[ 36%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o
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 In file included from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64,
                  from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19:
 /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain<T>::optimal_path() [with T = long unsigned int]':
@@ -814,22 +877,6 @@
 /usr/include/c++/12/bits/stl_iterator.h:458:5: note: declared here
   458 |     operator!=(const reverse_iterator<_Iterator>& __x,
       |     ^~~~~~~~
-[ 44%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o
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-[ 46%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o
-/usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
-/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core':
-/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow]
-  336 |         save_bin = save_tid = last_tid = last_bin = 0xffffffffu;
-      |                                          ^~~~~~~~
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-/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
-/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
-  678 |         fread(buf, 1, 28, fp->file);
-      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
 /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)':
 /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations]
    36 |   arma::set_stream_err1(null_ostream);
@@ -845,10 +892,6 @@
 /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here
   103 | set_stream_err2(std::ostream& user_stream)
       | ^~~~~~~~~~~~~~~
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-[ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o
-/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp
 make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
 [ 64%] Built target tvcassembly
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@@ -904,19 +947,19 @@
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 [ 86%] Building CXX object CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o
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-[ 89%] Linking CXX executable tvcutils
+[ 87%] Linking CXX executable tvcutils
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 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils  -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder 
+make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
+[ 87%] Built target tvcutils
+[ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o
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 [ 92%] Building CXX object CMakeFiles/tvc.dir/realignment/Realigner.cpp.o
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-make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
-[ 93%] Built target tvcutils
 [ 95%] Building C object CMakeFiles/tvc.dir/file-io/ion_error.c.o
 /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_error.c.o -MF CMakeFiles/tvc.dir/file-io/ion_error.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c
 [ 96%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o
@@ -932,10 +975,10 @@
 /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles 0
 make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
    dh_auto_test
-	cd obj-x86_64-linux-gnu && make -j16 test ARGS\+=--verbose ARGS\+=-j16
+	cd obj-x86_64-linux-gnu && make -j15 test ARGS\+=--verbose ARGS\+=-j15
 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
 Running tests...
-/usr/bin/ctest --force-new-ctest-process --verbose -j16
+/usr/bin/ctest --force-new-ctest-process --verbose -j15
 UpdateCTestConfiguration  from :/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl
 UpdateCTestConfiguration  from :/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/DartConfiguration.tcl
 Test project /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu
@@ -1283,6 +1326,9 @@
 2: SampleManager: Found 1 read group(s) and 1 sample(s).
 2: SampleManager: Primary sample "85" (default) present in 1 read group(s)
 2: TVC found a total of 1 different flow orders of max flow lengths: 500
+2: Recalibration was detected from comment lines in bam file(s):
+2: 1 unique blocks of recalibration info detected.
+2: Loading systematic error contexts.
 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
 3: 
 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
@@ -1437,6 +1483,9 @@
 3: SampleManager: Found 1 read group(s) and 1 sample(s).
 3: SampleManager: Primary sample "85" (default) present in 1 read group(s)
 3: TVC found a total of 1 different flow orders of max flow lengths: 500
+3: Recalibration was detected from comment lines in bam file(s):
+3: 1 unique blocks of recalibration info detected.
+3: Loading systematic error contexts.
 4: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
 4: 
 4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
@@ -1591,6 +1640,9 @@
 4: SampleManager: Found 1 read group(s) and 1 sample(s).
 4: SampleManager: Primary sample "85" (default) present in 1 read group(s)
 4: TVC found a total of 1 different flow orders of max flow lengths: 500
+4: Recalibration was detected from comment lines in bam file(s):
+4: 1 unique blocks of recalibration info detected.
+4: Loading systematic error contexts.
 5: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
 5: 
 5: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
@@ -1745,6 +1797,9 @@
 5: SampleManager: Found 1 read group(s) and 1 sample(s).
 5: SampleManager: Primary sample "85" (default) present in 1 read group(s)
 5: TVC found a total of 1 different flow orders of max flow lengths: 500
+5: Recalibration was detected from comment lines in bam file(s):
+5: 1 unique blocks of recalibration info detected.
+5: Loading systematic error contexts.
 6: 
 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
 6: 
@@ -1789,10 +1844,6 @@
 8:      --merged-plain-bed          FILE       output a valid plain merged BED [none]
 8:      --effective-bed             FILE       output a valid effective BED [none]
 8: 
- 1/10 Test  #1: tvc_call .........................................   Passed    0.02 sec
- 2/10 Test  #6: tvcutils_call ....................................   Passed    0.02 sec
- 3/10 Test  #7: tvcutils_prepare_hotspots_call ...................   Passed    0.01 sec
- 4/10 Test  #8: tvcutils_validate_bed_call .......................   Passed    0.01 sec
 9: Parameter novel-tvc-vcf is required and empty.
 9: 
 9: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
@@ -1811,7 +1862,6 @@
 9:   -d,--input-depth               FILE       output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok)
 9:   -m,--min-depth                 INT        minimum coverage depth in GVCF output (optional)
 9: 
- 5/10 Test  #9: tvcutils_unify_vcf_call ..........................   Passed    0.01 sec
 10: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly
 10: 
 10: Usage: tvcassembly [options]
@@ -1838,50 +1888,43 @@
 10:      --relative_strand_bias             FLOAT       (stbias) Variants with strand bias above this are not reported [0.80].
 10:      --output_mnv                       INT         (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0].
 10: 
- 6/10 Test #10: tvcassembly_call .................................   Passed    0.01 sec
-2: Recalibration was detected from comment lines in bam file(s):
-2: 1 unique blocks of recalibration info detected.
-2: Loading systematic error contexts.
-3: Recalibration was detected from comment lines in bam file(s):
-3: 1 unique blocks of recalibration info detected.
-3: Loading systematic error contexts.
-4: Recalibration was detected from comment lines in bam file(s):
-4: 1 unique blocks of recalibration info detected.
-4: Loading systematic error contexts.
-5: Recalibration was detected from comment lines in bam file(s):
-5: 1 unique blocks of recalibration info detected.
-5: Loading systematic error contexts.
+ 1/10 Test  #1: tvc_call .........................................   Passed    0.19 sec
+ 2/10 Test  #6: tvcutils_call ....................................   Passed    0.09 sec
+ 3/10 Test  #7: tvcutils_prepare_hotspots_call ...................   Passed    0.08 sec
+ 4/10 Test  #8: tvcutils_validate_bed_call .......................   Passed    0.06 sec
+ 5/10 Test  #9: tvcutils_unify_vcf_call ..........................   Passed    0.05 sec
+ 6/10 Test #10: tvcassembly_call .................................   Passed    0.03 sec
+3: Loaded.
 2: Loaded.
-5: Loaded.
 4: Loaded.
-3: Loaded.
-2: Recalibration model: suppressed
-2: 
-2: 
-2: [tvc] Normal termination. Processing time: 1 seconds.
 3: Recalibration model: suppressed
 3: 
 3: 
-3: [tvc] Normal termination. Processing time: 1 seconds.
+3: [tvc] Normal termination. Processing time: 2 seconds.
+5: Loaded.
+2: Recalibration model: suppressed
+2: 
+2: 
+2: [tvc] Normal termination. Processing time: 3 seconds.
+ 7/10 Test  #3: tvc_test_1_thread_sse_off ........................   Passed    2.90 sec
 5: 
 5: 
-5: [tvc] Normal termination. Processing time: 1 seconds.
+5: [tvc] Normal termination. Processing time: 3 seconds.
 4: 
 4: 
-4: [tvc] Normal termination. Processing time: 1 seconds.
- 7/10 Test  #3: tvc_test_1_thread_sse_off ........................   Passed    1.31 sec
- 8/10 Test  #2: tvc_test_1_thread_sse_on .........................   Passed    1.34 sec
- 9/10 Test  #5: tvc_test_4_threads_sse_off_with_parameter_file ...   Passed    1.43 sec
-10/10 Test  #4: tvc_test_4_threads_sse_on_with_parameter_file ....   Passed    1.45 sec
+4: [tvc] Normal termination. Processing time: 3 seconds.
+ 8/10 Test  #2: tvc_test_1_thread_sse_on .........................   Passed    3.30 sec
+ 9/10 Test  #5: tvc_test_4_threads_sse_off_with_parameter_file ...   Passed    3.28 sec
+10/10 Test  #4: tvc_test_4_threads_sse_on_with_parameter_file ....   Passed    3.79 sec
 
 100% tests passed, 0 tests failed out of 10
 
-Total Test time (real) =   1.46 sec
+Total Test time (real) =   3.85 sec
 make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
    create-stamp debian/debhelper-build-stamp
    dh_prep
    dh_auto_install --destdir=debian/tvc/
-	cd obj-x86_64-linux-gnu && make -j16 install DESTDIR=/build/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
+	cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu'
 /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
 make  -f CMakeFiles/Makefile2 preinstall
@@ -1940,8 +1983,8 @@
    dh_gencontrol
    dh_md5sums
    dh_builddeb
-dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.deb'.
 dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_amd64.deb'.
+dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.deb'.
  dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.buildinfo
  dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.changes
 dpkg-genchanges: info: binary-only upload (no source code included)
@@ -1949,12 +1992,14 @@
 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/1180282/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/1180282/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/621218 and its subdirectories
-I: Current time: Fri May 31 23:32:49 -12 2024
-I: pbuilder-time-stamp: 1717241569
+I: removing directory /srv/workspace/pbuilder/1180282 and its subdirectories
+I: Current time: Sun Apr 30 19:14:36 +14 2023
+I: pbuilder-time-stamp: 1682831676