I: pbuilder: network access will be disabled during build
I: Current time: Wed Jan 21 02:22:40 +14 2026
I: pbuilder-time-stamp: 1768911760
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: using eatmydata during job
I: Copying source file
I: copying [smalt_0.7.6-13.dsc]
I: copying [./smalt_0.7.6.orig.tar.gz]
I: copying [./smalt_0.7.6-13.debian.tar.xz]
I: Extracting source
gpgv: Signature made Fri Jan 12 06:08:11 2024 
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./smalt_0.7.6-13.dsc: no acceptable signature found
dpkg-source: info: extracting smalt in smalt-0.7.6
dpkg-source: info: unpacking smalt_0.7.6.orig.tar.gz
dpkg-source: info: unpacking smalt_0.7.6-13.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying add-runstatedir.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/120264/tmp/hooks/D01_modify_environment starting
debug: Running on ionos16-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 20 12:22 /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/120264/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/120264/tmp/hooks/D02_print_environment starting
I: set
  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=21 '
  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=dd5ce64c1a6146989ce8654f5998c945
  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=120264
  PS4='+ '
  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.vkhNRO3r/pbuilderrc_ikm1 --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.vkhNRO3r/b2 --logfile b2/build.log smalt_0.7.6-13.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://213.165.73.152:3128
I: uname -a
  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/120264/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: i386
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), zlib1g-dev, python3, samtools, libbambamc-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19952 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
  Package zlib1g-dev is not installed.
 pbuilder-satisfydepends-dummy depends on python3; however:
  Package python3 is not installed.
 pbuilder-satisfydepends-dummy depends on samtools; however:
  Package samtools is not installed.
 pbuilder-satisfydepends-dummy depends on libbambamc-dev; however:
  Package libbambamc-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbambamc-dev{a} libbambamc0{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libnsl2{a} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtirpc-common{a} libtirpc3t64{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.12{a} python3.12-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 
0 packages upgraded, 75 newly installed, 0 to remove and 0 not upgraded.
Need to get 31.6 MB of archives. After unpacking 114 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main i386 libpython3.12-minimal i386 3.12.8-3 [816 kB]
Get: 2 http://deb.debian.org/debian unstable/main i386 libexpat1 i386 2.6.4-1 [107 kB]
Get: 3 http://deb.debian.org/debian unstable/main i386 python3.12-minimal i386 3.12.8-3 [2239 kB]
Get: 4 http://deb.debian.org/debian unstable/main i386 python3-minimal i386 3.12.7-1 [26.8 kB]
Get: 5 http://deb.debian.org/debian unstable/main i386 media-types all 10.1.0 [26.9 kB]
Get: 6 http://deb.debian.org/debian unstable/main i386 netbase all 6.4 [12.8 kB]
Get: 7 http://deb.debian.org/debian unstable/main i386 tzdata all 2024b-4 [256 kB]
Get: 8 http://deb.debian.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB]
Get: 9 http://deb.debian.org/debian unstable/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB]
Get: 11 http://deb.debian.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-4 [9600 B]
Get: 12 http://deb.debian.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-3 [350 kB]
Get: 13 http://deb.debian.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB]
Get: 14 http://deb.debian.org/debian unstable/main i386 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB]
Get: 15 http://deb.debian.org/debian unstable/main i386 libtirpc3t64 i386 1.3.4+ds-1.3+b1 [90.5 kB]
Get: 16 http://deb.debian.org/debian unstable/main i386 libnsl2 i386 1.3.0-3+b3 [42.7 kB]
Get: 17 http://deb.debian.org/debian unstable/main i386 readline-common all 8.2-6 [69.4 kB]
Get: 18 http://deb.debian.org/debian unstable/main i386 libreadline8t64 i386 8.2-6 [173 kB]
Get: 19 http://deb.debian.org/debian unstable/main i386 libpython3.12-stdlib i386 3.12.8-3 [1968 kB]
Get: 20 http://deb.debian.org/debian unstable/main i386 python3.12 i386 3.12.8-3 [677 kB]
Get: 21 http://deb.debian.org/debian unstable/main i386 libpython3-stdlib i386 3.12.7-1 [9712 B]
Get: 22 http://deb.debian.org/debian unstable/main i386 python3 i386 3.12.7-1 [27.8 kB]
Get: 23 http://deb.debian.org/debian unstable/main i386 sensible-utils all 0.0.24 [24.8 kB]
Get: 24 http://deb.debian.org/debian unstable/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB]
Get: 25 http://deb.debian.org/debian unstable/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB]
Get: 26 http://deb.debian.org/debian unstable/main i386 file i386 1:5.45-3+b1 [43.2 kB]
Get: 27 http://deb.debian.org/debian unstable/main i386 gettext-base i386 0.22.5-3 [201 kB]
Get: 28 http://deb.debian.org/debian unstable/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB]
Get: 29 http://deb.debian.org/debian unstable/main i386 groff-base i386 1.23.0-6 [1198 kB]
Get: 30 http://deb.debian.org/debian unstable/main i386 bsdextrautils i386 2.40.2-12 [95.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB]
Get: 32 http://deb.debian.org/debian unstable/main i386 man-db i386 2.13.0-1 [1428 kB]
Get: 33 http://deb.debian.org/debian unstable/main i386 m4 i386 1.4.19-4 [293 kB]
Get: 34 http://deb.debian.org/debian unstable/main i386 autoconf all 2.72-3 [493 kB]
Get: 35 http://deb.debian.org/debian unstable/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 36 http://deb.debian.org/debian unstable/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 37 http://deb.debian.org/debian unstable/main i386 autopoint all 0.22.5-3 [723 kB]
Get: 38 http://deb.debian.org/debian unstable/main i386 libdebhelper-perl all 13.21 [88.9 kB]
Get: 39 http://deb.debian.org/debian unstable/main i386 libtool all 2.4.7-8 [517 kB]
Get: 40 http://deb.debian.org/debian unstable/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 41 http://deb.debian.org/debian unstable/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 42 http://deb.debian.org/debian unstable/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get: 43 http://deb.debian.org/debian unstable/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get: 44 http://deb.debian.org/debian unstable/main i386 libelf1t64 i386 0.192-4 [195 kB]
Get: 45 http://deb.debian.org/debian unstable/main i386 dwz i386 0.15-1+b1 [116 kB]
Get: 46 http://deb.debian.org/debian unstable/main i386 libicu72 i386 72.1-5+b1 [9583 kB]
Get: 47 http://deb.debian.org/debian unstable/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB]
Get: 48 http://deb.debian.org/debian unstable/main i386 gettext i386 0.22.5-3 [1631 kB]
Get: 49 http://deb.debian.org/debian unstable/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 51 http://deb.debian.org/debian unstable/main i386 debhelper all 13.21 [919 kB]
Get: 52 http://deb.debian.org/debian unstable/main i386 libbambamc0 i386 0.0.50-6+b2 [43.7 kB]
Get: 53 http://deb.debian.org/debian unstable/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB]
Get: 54 http://deb.debian.org/debian unstable/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB]
Get: 55 http://deb.debian.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get: 56 http://deb.debian.org/debian unstable/main i386 pkg-config i386 1.8.1-4 [14.0 kB]
Get: 57 http://deb.debian.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get: 58 http://deb.debian.org/debian unstable/main i386 libbambamc-dev i386 0.0.50-6+b2 [58.4 kB]
Get: 59 http://deb.debian.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB]
Get: 60 http://deb.debian.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB]
Get: 61 http://deb.debian.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB]
Get: 62 http://deb.debian.org/debian unstable/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB]
Get: 63 http://deb.debian.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB]
Get: 64 http://deb.debian.org/debian unstable/main i386 libnghttp3-9 i386 1.6.0-2 [75.9 kB]
Get: 65 http://deb.debian.org/debian unstable/main i386 libngtcp2-16 i386 1.9.1-1 [151 kB]
Get: 66 http://deb.debian.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.9.1-1 [19.1 kB]
Get: 67 http://deb.debian.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get: 68 http://deb.debian.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB]
Get: 69 http://deb.debian.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get: 70 http://deb.debian.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.11.1-1 [404 kB]
Get: 71 http://deb.debian.org/debian unstable/main i386 libdeflate0 i386 1.22-1 [48.1 kB]
Get: 72 http://deb.debian.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-1 [70.8 kB]
Get: 73 http://deb.debian.org/debian unstable/main i386 libhts3t64 i386 1.20+ds-2 [500 kB]
Get: 74 http://deb.debian.org/debian unstable/main i386 libncurses6 i386 6.5-2+b1 [112 kB]
Get: 75 http://deb.debian.org/debian unstable/main i386 samtools i386 1.20-3 [688 kB]
Fetched 31.6 MB in 0s (75.3 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.12-minimal:i386.
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(Reading database ... 19952 files and directories currently installed.)
Preparing to unpack .../libpython3.12-minimal_3.12.8-3_i386.deb ...
Unpacking libpython3.12-minimal:i386 (3.12.8-3) ...
Selecting previously unselected package libexpat1:i386.
Preparing to unpack .../libexpat1_2.6.4-1_i386.deb ...
Unpacking libexpat1:i386 (2.6.4-1) ...
Selecting previously unselected package python3.12-minimal.
Preparing to unpack .../python3.12-minimal_3.12.8-3_i386.deb ...
Unpacking python3.12-minimal (3.12.8-3) ...
Setting up libpython3.12-minimal:i386 (3.12.8-3) ...
Setting up libexpat1:i386 (2.6.4-1) ...
Setting up python3.12-minimal (3.12.8-3) ...
Selecting previously unselected package python3-minimal.
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(Reading database ... 20272 files and directories currently installed.)
Preparing to unpack .../00-python3-minimal_3.12.7-1_i386.deb ...
Unpacking python3-minimal (3.12.7-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../01-media-types_10.1.0_all.deb ...
Unpacking media-types (10.1.0) ...
Selecting previously unselected package netbase.
Preparing to unpack .../02-netbase_6.4_all.deb ...
Unpacking netbase (6.4) ...
Selecting previously unselected package tzdata.
Preparing to unpack .../03-tzdata_2024b-4_all.deb ...
Unpacking tzdata (2024b-4) ...
Selecting previously unselected package libkrb5support0:i386.
Preparing to unpack .../04-libkrb5support0_1.21.3-3_i386.deb ...
Unpacking libkrb5support0:i386 (1.21.3-3) ...
Selecting previously unselected package libcom-err2:i386.
Preparing to unpack .../05-libcom-err2_1.47.2~rc1-2_i386.deb ...
Unpacking libcom-err2:i386 (1.47.2~rc1-2) ...
Selecting previously unselected package libk5crypto3:i386.
Preparing to unpack .../06-libk5crypto3_1.21.3-3_i386.deb ...
Unpacking libk5crypto3:i386 (1.21.3-3) ...
Selecting previously unselected package libkeyutils1:i386.
Preparing to unpack .../07-libkeyutils1_1.6.3-4_i386.deb ...
Unpacking libkeyutils1:i386 (1.6.3-4) ...
Selecting previously unselected package libkrb5-3:i386.
Preparing to unpack .../08-libkrb5-3_1.21.3-3_i386.deb ...
Unpacking libkrb5-3:i386 (1.21.3-3) ...
Selecting previously unselected package libgssapi-krb5-2:i386.
Preparing to unpack .../09-libgssapi-krb5-2_1.21.3-3_i386.deb ...
Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ...
Selecting previously unselected package libtirpc-common.
Preparing to unpack .../10-libtirpc-common_1.3.4+ds-1.3_all.deb ...
Unpacking libtirpc-common (1.3.4+ds-1.3) ...
Selecting previously unselected package libtirpc3t64:i386.
Preparing to unpack .../11-libtirpc3t64_1.3.4+ds-1.3+b1_i386.deb ...
Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3 to /lib/i386-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64'
Adding 'diversion of /lib/i386-linux-gnu/libtirpc.so.3.0.0 to /lib/i386-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
Unpacking libtirpc3t64:i386 (1.3.4+ds-1.3+b1) ...
Selecting previously unselected package libnsl2:i386.
Preparing to unpack .../12-libnsl2_1.3.0-3+b3_i386.deb ...
Unpacking libnsl2:i386 (1.3.0-3+b3) ...
Selecting previously unselected package readline-common.
Preparing to unpack .../13-readline-common_8.2-6_all.deb ...
Unpacking readline-common (8.2-6) ...
Selecting previously unselected package libreadline8t64:i386.
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Adding 'diversion of /lib/i386-linux-gnu/libhistory.so.8 to /lib/i386-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64'
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Setting up tzdata (2024b-4) ...

Current default time zone: 'Etc/UTC'
Local time is now:      Tue Jan 20 12:23:02 UTC 2026.
Universal Time is now:  Tue Jan 20 12:23:02 UTC 2026.
Run 'dpkg-reconfigure tzdata' if you wish to change it.

Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:i386 (1.8.1-4) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ...
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Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up dwz (0.15-1+b1) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Not building database; man-db/auto-update is not 'true'.
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Setting up python3 (3.12.7-1) ...
Processing triggers for libc-bin (2.40-4) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/120264/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/120264/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/smalt-0.7.6/ && 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  > ../smalt_0.7.6-13_source.changes
dpkg-buildpackage: info: source package smalt
dpkg-buildpackage: info: source version 0.7.6-13
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_clean
rm -rf test/*.pyc misc/*.pyc test/tmp
find . -type d -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   debian/rules override_dh_autoreconf
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
echo "Do nothing - fails because auf broken upstream autoconf stuff"
Do nothing - fails because auf broken upstream autoconf stuff
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_configure -- CONFIG_SHELL=/bin/bash
	./configure --build=i686-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/i386-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking CONFIG_SHELL=/bin/bash
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking for icc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... none
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ranlib... ranlib
checking for a Python interpreter with version >= 2.6... python3
checking for python3... /usr/bin/python3
checking for python3 version... 3.1
checking for python3 platform... linux
checking for python3 script directory... ${prefix}/lib/python3.1/site-packages
checking for python3 extension module directory... ${exec_prefix}/lib/python3.1/site-packages
checking for samtools... yes
checking for sam_open in -lbam... no
checking for BAMBAMC... yes
checking for gzread in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking semaphore.h usability... yes
checking semaphore.h presence... yes
checking for semaphore.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for stdint.h... (cached) yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking emmintrin.h usability... yes
checking emmintrin.h presence... yes
checking for emmintrin.h... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating test/Makefile
config.status: creating test/data/Makefile
config.status: creating misc/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   debian/rules override_dh_auto_build-arch
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_auto_build -a
	make -j21
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make  all-recursive
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making all in src
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c elib.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c filio.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c sequence.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-score.o `test -f 'score.c' || echo './'`score.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-diffstr.o `test -f 'diffstr.c' || echo './'`diffstr.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alibuffer.o `test -f 'alibuffer.c' || echo './'`alibuffer.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-alignment.o `test -f 'alignment.c' || echo './'`alignment.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-swsimd.o `test -f 'swsimd.c' || echo './'`swsimd.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-sort.o `test -f 'sort.c' || echo './'`sort.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-array.o `test -f 'array.c' || echo './'`array.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-interval.o `test -f 'interval.c' || echo './'`interval.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashidx.o `test -f 'hashidx.c' || echo './'`hashidx.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-hashhit.o `test -f 'hashhit.c' || echo './'`hashhit.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra   -msse2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o libsgm_a-segment.o `test -f 'segment.c' || echo './'`segment.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-smalt.o `test -f 'smalt.c' || echo './'`smalt.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-menu.o `test -f 'menu.c' || echo './'`menu.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-threads.o `test -f 'threads.c' || echo './'`threads.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-infmt.o `test -f 'infmt.c' || echo './'`infmt.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-results.o `test -f 'results.c' || echo './'`results.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-resultpairs.o `test -f 'resultpairs.c' || echo './'`resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-report.o `test -f 'report.c' || echo './'`report.c
diffstr.c: In function 'diffStrGetDiffStats':
diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress]
  978 |       if (diffstrp+1 != NULL) {
      |                      ^~
hashidx.c: In function 'countPerfectKey':
hashidx.c:191:77: warning: unused parameter 'tuplectr' [-Wunused-parameter]
  191 | static int countPerfectKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
      |                                                                   ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countCollisionKey':
hashidx.c:206:79: warning: unused parameter 'tuplectr' [-Wunused-parameter]
  206 | static int countCollisionKey(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
      |                                                                     ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'collectWords':
hashidx.c:223:74: warning: unused parameter 'tuplectr' [-Wunused-parameter]
  223 | static int collectWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
      |                                                                ~~~~~~~~~~^~~~~~~~
hashidx.c: In function 'countWords':
hashidx.c:265:72: warning: unused parameter 'tuplectr' [-Wunused-parameter]
  265 | static int countWords(const HashTable *htp, HASHWORD_t word, HASHPOS_t tuplectr)
      |                                                              ~~~~~~~~~~^~~~~~~~
hashhit.c: In function 'hashCreateHitList':
hashhit.c:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'enum <anonymous>' [-Wsign-compare]
 1559 |     if (maxnhits < HITLST_MINSIZ) maxnhits = HITLST_MINSIZ;
      |                  ^
sequence.c: In function 'make3BitMangledCodec':
sequence.c:298:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
  298 |   for (i=1; i<SIZE_CODTAB; i++) {
      |              ^
sequence.c: In function 'seqCodecCreateFromAlphabet':
sequence.c:372:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
  372 |   for (i=0; i<SIZE_DECODTAB; i++)
      |              ^
sequence.c:378:14: warning: comparison of integer expressions of different signedness: 'int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
  378 |   for (i=0; i<SIZE_CODTAB; i++) {
      |              ^
hashidx.c: At top level:
hashidx.c:446:18: warning: 'getWordHisto' defined but not used [-Wunused-function]
  446 | static WORDNUM_t getWordHisto(WORDNUM_t *counts, HASHNUM_t n, const HashTable *htp)
      |                  ^~~~~~~~~~~~
hashidx.c:63:19: warning: 'HASHTABFIL_READERRMSG' defined but not used [-Wunused-const-variable=]
   63 | static const char HASHTABFIL_READERRMSG[] = "when reading hash table file";
      |                   ^~~~~~~~~~~~~~~~~~~~~
sequence.c: In function 'fprintSeqFastqSequence':
sequence.c:1700:16: warning: comparison of integer expressions of different signedness: 'short int' and 'enum SEQ_CONSTANTS' [-Wsign-compare]
 1700 |   if (linewidth>OUTBUFSIZE) linewidth = OUTBUFSIZE;
      |                ^
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-rmap.o `test -f 'rmap.c' || echo './'`rmap.c
score.c:49:21: warning: 'LN0P25' defined but not used [-Wunused-const-variable=]
   49 | static const double LN0P25 = -1.386294; /* natural logarithm of 1/4 */
      |                     ^~~~~~
segment.c:1375:12: warning: 'checkCANDARRsequential' defined but not used [-Wunused-function]
 1375 | static int checkCANDARRsequential(const CANDARR candr, SEGNUM_t *rvc_offs)
      |            ^~~~~~~~~~~~~~~~~~~~~~
segment.c:1330:13: warning: 'labelSEGCANDWithinInsertRange' defined but not used [-Wunused-function]
 1330 | static void labelSEGCANDWithinInsertRange (SEGCAND *candAp, SEGNUM_t nsegA,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
sequence.c: In function 'seqFastqGetConstSequence':
sequence.c:2079:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2079 |       if (length)
      |       ^~
sequence.c:2081:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2081 |         return NULL;
      |         ^~~~~~
sequence.c: In function 'seqFastqGetSequence':
sequence.c:2094:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
 2094 |       if (length)
      |       ^~
alignment.c:478:13: warning: 'blankALITRACK' defined but not used [-Wunused-function]
  478 | static void blankALITRACK(ALITRACK *trackp, const ALIBAND *bandp)
      |             ^~~~~~~~~~~~~
sequence.c:2096:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
 2096 |         return NULL;
      |         ^~~~~~
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt-insert.o `test -f 'insert.c' || echo './'`insert.c
smalt.c: In function 'cleanupSmaltOutput':
smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
  659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
      |                               ~~~~~~~~^~~~~~~
sequence.c: In function 'seqIOopen':
sequence.c:489:5: warning: this statement may fall through [-Wimplicit-fallthrough=]
  489 |     strcpy(p->fmode, "r");
      |     ^~~~~~~~~~~~~~~~~~~~~
sequence.c:491:3: note: here
  491 |   case SEQIO_WRITE_GZIP_FASTA:
      |   ^~~~
rm -f libseq.a
ar cru libseq.a elib.o filio.o sequence.o 
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libseq.a
rm -f libsgm.a
ar cru libsgm.a libsgm_a-score.o libsgm_a-diffstr.o libsgm_a-alibuffer.o libsgm_a-alignment.o libsgm_a-swsimd.o libsgm_a-sort.o libsgm_a-array.o libsgm_a-interval.o libsgm_a-hashidx.o libsgm_a-hashhit.o libsgm_a-segment.o libseq.a
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libsgm.a
gcc  -Wall -Wextra   -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security    -Wl,-z,relro -Wl,-z,now -o smalt smalt-smalt.o smalt-menu.o smalt-threads.o smalt-infmt.o smalt-results.o smalt-resultpairs.o smalt-report.o smalt-rmap.o smalt-insert.o libsgm.a libseq.a -lbambamc -lz -lm -lpthread -lz	 
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making all in test
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[5]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[5]: Nothing to be done for 'all-am'.
make[5]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making all in misc
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c simread.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c rsample.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c fetchseq.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c splitreads.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c mixreads.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c splitmates.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c readstats.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c trunkreads.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c basqcol.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c basqual.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c simqual.c
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o diffstr.o `test -f '../src/diffstr.c' || echo './'`../src/diffstr.c
../src/diffstr.c: In function 'diffStrGetDiffStats':
../src/diffstr.c:978:22: warning: the comparison will always evaluate as 'true' for the pointer operand in 'diffstrp + 1' must not be NULL [-Waddress]
  978 |       if (diffstrp+1 != NULL) {
      |                      ^~
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o readstats readstats.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o trunkreads trunkreads.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o splitmates splitmates.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o fetchseq fetchseq.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o splitreads splitreads.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o mixreads mixreads.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o basqcol basqcol.o basqual.o ../src/libseq.a -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o simread simread.o rsample.o ../src/libsgm.a ../src/libseq.a -lm -lz 
gcc -I../src/    -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o simqual simqual.o basqual.o diffstr.o ../src/libseq.a -lm -lz 
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make -C test sequenceReverseComplement_test
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
gcc -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c sequenceReverseComplement_test.c
gcc -I../src/ -I../test   -Wall -Wextra  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security  -Wl,-z,relro -Wl,-z,now -o sequenceReverseComplement_test sequenceReverseComplement_test.o ../src/libseq.a -lz 
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   dh_auto_build -Nsmalt
	make -j21
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make  all-recursive
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making all in src
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making all in test
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making all in misc
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   dh_auto_test
	make -j21 check "TESTSUITEFLAGS=-j21 --verbose" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
Making check in src
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/src'
Making check in test
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make  sequenceReverseComplement_test smalt_Xali_test    
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
make[4]: 'sequenceReverseComplement_test' is up to date.
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-smalt.o `test -f '../src/smalt.c' || echo './'`../src/smalt.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-menu.o `test -f '../src/menu.c' || echo './'`../src/menu.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-threads.o `test -f '../src/threads.c' || echo './'`../src/threads.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-infmt.o `test -f '../src/infmt.c' || echo './'`../src/infmt.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-results.o `test -f '../src/results.c' || echo './'`../src/results.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-resultpairs.o `test -f '../src/resultpairs.c' || echo './'`../src/resultpairs.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-insert.o `test -f '../src/insert.c' || echo './'`../src/insert.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-report.o `test -f '../src/report.c' || echo './'`../src/report.c
gcc -DHAVE_CONFIG_H -I. -I..  -DSMALT_DEBUG_XALI -Wdate-time -D_FORTIFY_SOURCE=2 -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security -c -o smalt_Xali_test-rmap.o `test -f '../src/rmap.c' || echo './'`../src/rmap.c
../src/smalt.c: In function 'cleanupSmaltOutput':
../src/smalt.c:659:39: warning: unused parameter 'errmsgp' [-Wunused-parameter]
  659 | static int cleanupSmaltOutput(ErrMsg *errmsgp, void *op)
      |                               ~~~~~~~~^~~~~~~
gcc -I../src/ -I../test   -Wall -Wextra  -msse2  -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/smalt-0.7.6=. -fstack-protector-strong -Wformat -Werror=format-security   -Wl,-z,relro -Wl,-z,now -o smalt_Xali_test smalt_Xali_test-smalt.o smalt_Xali_test-menu.o smalt_Xali_test-threads.o smalt_Xali_test-infmt.o smalt_Xali_test-results.o smalt_Xali_test-resultpairs.o smalt_Xali_test-insert.o smalt_Xali_test-report.o smalt_Xali_test-rmap.o ../src/libsgm.a ../src/libseq.a -lbambamc -lz -lm -lpthread -lz 
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make  check-TESTS
make[4]: Entering directory '/build/reproducible-path/smalt-0.7.6/test'
/build/reproducible-path/smalt-0.7.6/test/formats.py:32: SyntaxWarning: invalid escape sequence '\d'
  CIGARSTR = compile("^cigar:([ABCDNRSP]):(\d{2})\s+(\S+)\s+(\d+)\s+(\d+)\s+([*+-])\s+" \
/build/reproducible-path/smalt-0.7.6/test/formats.py:33: SyntaxWarning: invalid escape sequence '\S'
  "(\S+)\s+(\d+)\s+(\d+)\s+\+\s+(\d+)\s+(.+)$")
PASS: splitReads_test.py
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:13: SyntaxWarning: invalid escape sequence '\d'
  "Bbf^BcfBbdcfBdcfcddYbaB\dfYcc\ec_efeed\_cTebcacced"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:14: SyntaxWarning: invalid escape sequence '\e'
  "bebf`^fa^cV`fde^\ecc`d`cbccfeTbdbeZcefccf^fccbfBc!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:20: SyntaxWarning: invalid escape sequence '\`'
  "edff^Yc^`dY`\\fefa^ddcYb^ef`adfdB\`f\`c`defce`adde!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:25: SyntaxWarning: invalid escape sequence '\B'
  "Yfffcc\BYBf`dedBeeaZf^c^adff`BbfeTB_bdf\`YfdeBfBdd"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:26: SyntaxWarning: invalid escape sequence '\e'
  "eB_ae\eVff]dTedc_dcff^cVa_^d\\affdfdfddcadbbBT^fBd!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:32: SyntaxWarning: invalid escape sequence '\c'
  "B``bdZffbeMUcUaTfeceb`V^fecaddde\cfW^de[Bececec`B!\n",
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:37: SyntaxWarning: invalid escape sequence '\e'
  "daBZddeYdBfe`fBf`ecfdfcf`c\eacXdbLe^b``ccadK]e]^_T"\
/build/reproducible-path/smalt-0.7.6/test/./results_split_test.py:38: SyntaxWarning: invalid escape sequence '\T'
  "fccbcd\Tffb^Yfdfdf^efa\[fbfdad`X\\Ue_^eBfcfcfNfdf^!\n"
PASS: results_split_test.py
PASS: ouform_cigar_test.py
PASS: sample_test.py
PASS: cigar_test.py
PASS: mthread_test.py
PASS: ioform_test.py
/build/reproducible-path/smalt-0.7.6/test/./xali_test.py:76: SyntaxWarning: invalid escape sequence '\S'
  REFNAMNO = compile("^\S+_(\d+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:5: SyntaxWarning: invalid escape sequence '\S'
  SAMSTR = re.compile("^(\S+)\t(\d+)\t(\S+)\t(\d+)\t(\d+)\t(\S+)\t(\S+)\t"\
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:6: SyntaxWarning: invalid escape sequence '\d'
  "(\d+)\t([\+\-]*\d+)\t(\S+)\t(\S+)"\
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:8: SyntaxWarning: invalid escape sequence '\S'
  TAGSTR = re.compile("^(\S{2}):([iZ]):(\S+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:13: SyntaxWarning: invalid escape sequence '\S'
  QNAMSTR = re.compile("^(\S+)\/([12])$")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:14: SyntaxWarning: invalid escape sequence '\d'
  ALISCOR = re.compile("\tAS:i:(\d+)")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:15: SyntaxWarning: invalid escape sequence '\d'
  CLIPSTART = re.compile("^(\d+)([HS])")
/build/reproducible-path/smalt-0.7.6/test/../misc/SAM.py:16: SyntaxWarning: invalid escape sequence '\d'
  CLIPEND   = re.compile("(\d+)([HS])$")
PASS: xali_test.py
PASS: bam_cigar_test.py
==================
All 9 tests passed
==================
make[4]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[3]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/test'
Making check in misc
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6/misc'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6/misc'
make[2]: Entering directory '/build/reproducible-path/smalt-0.7.6'
make[2]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
# upstream install does install more files than needed
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   debian/rules override_dh_install-indep
make[1]: Entering directory '/build/reproducible-path/smalt-0.7.6'
dh_install
# fix path to smalt executable in examples
for py in `ls test/*.py` ; do \
    sed 's#PROGNAM = "../src/smalt"#PROGNAM = "/usr/bin/smalt"#' ${py} > debian/smalt-examples/usr/share/doc/smalt/${py} ; \
done
make[1]: Leaving directory '/build/reproducible-path/smalt-0.7.6'
   dh_install -Nsmalt-examples
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
dwz: debian/smalt/usr/bin/smalt: DWARF compression not beneficial - old size 241265 new size 245119
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'smalt' in '../smalt_0.7.6-13_i386.deb'.
dpkg-deb: building package 'smalt-dbgsym' in '../smalt-dbgsym_0.7.6-13_i386.deb'.
dpkg-deb: building package 'smalt-examples' in '../smalt-examples_0.7.6-13_all.deb'.
 dpkg-genbuildinfo --build=binary -O../smalt_0.7.6-13_i386.buildinfo
 dpkg-genchanges --build=binary -O../smalt_0.7.6-13_i386.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
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/120264/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/120264/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/120264 and its subdirectories
I: Current time: Wed Jan 21 02:25:35 +14 2026
I: pbuilder-time-stamp: 1768911935