I: pbuilder: network access will be disabled during build
I: Current time: Thu Apr  2 15:03:49 +14 2026
I: pbuilder-time-stamp: 1775091829
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: Copying source file
I: copying [allelecount_4.3.0-3.dsc]
I: copying [./allelecount_4.3.0.orig.tar.gz]
I: copying [./allelecount_4.3.0-3.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./allelecount_4.3.0-3.dsc: unsupported subcommand
dpkg-source: info: extracting allelecount in allelecount-4.3.0
dpkg-source: info: unpacking allelecount_4.3.0.orig.tar.gz
dpkg-source: info: unpacking allelecount_4.3.0-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/3787794/tmp/hooks/D01_modify_environment starting
debug: Running on ionos15-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  2 01:04 /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/3787794/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/3787794/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]="x86_64-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=amd64
  DEBIAN_FRONTEND=noninteractive
  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=938a75ff47a9466b91511a2890631fc7
  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=3787794
  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.0ajFPrKe/pbuilderrc_hipb --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.0ajFPrKe/b2 --logfile b2/build.log allelecount_4.3.0-3.dsc'
  SUDO_GID=111
  SUDO_UID=106
  SUDO_USER=jenkins
  TERM=unknown
  TZ=/usr/share/zoneinfo/Etc/GMT-14
  UID=0
  USER=root
  _='I: set'
  http_proxy=http://213.165.73.152:3128
I: uname -a
  Linux i-capture-the-hostname 6.12.9+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.9-1~bpo12+1 (2025-01-19) 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/3787794/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: amd64
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), libhts-dev, libbz2-dev, libconst-fast-perl, libdevel-cover-perl, libfile-slurp-perl, libfile-which-perl, libipc-system-simple-perl, libjson-perl, libpod-coverage-perl, libtest-fatal-perl, libtry-tiny-perl, perl
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19779 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 libhts-dev; however:
  Package libhts-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libbz2-dev; however:
  Package libbz2-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libconst-fast-perl; however:
  Package libconst-fast-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libdevel-cover-perl; however:
  Package libdevel-cover-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libfile-slurp-perl; however:
  Package libfile-slurp-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libfile-which-perl; however:
  Package libfile-which-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libipc-system-simple-perl; however:
  Package libipc-system-simple-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libjson-perl; however:
  Package libjson-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libpod-coverage-perl; however:
  Package libpod-coverage-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libtest-fatal-perl; however:
  Package libtest-fatal-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libtry-tiny-perl; however:
  Package libtry-tiny-perl 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} comerr-dev{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} krb5-multidev{a} libarchive-zip-perl{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcom-err2{a} libconst-fast-perl{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdata-optlist-perl{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdevel-cover-perl{a} libdevel-symdump-perl{a} libelf1t64{a} libevent-2.1-7t64{a} libffi8{a} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libipc-system-simple-perl{a} libjson-perl{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} libldap-dev{a} libldap2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libngtcp2-16{a} libngtcp2-crypto-gnutls-dev{a} libngtcp2-crypto-gnutls8{a} libngtcp2-dev{a} libp11-kit-dev{a} libp11-kit0{a} libparams-util-perl{a} libpipeline1{a} libpkgconf3{a} libpod-coverage-perl{a} libpod-parser-perl{a} libpsl-dev{a} libpsl5t64{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-perl{a} libtasn1-6{a} libtasn1-6-dev{a} libtest-fatal-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunbound8{a} libunistring5{a} liburi-perl{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} sensible-utils{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libhttp-message-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc libtemplate-perl lynx publicsuffix wget 
0 packages upgraded, 113 newly installed, 0 to remove and 0 not upgraded.
Need to get 40.8 MB of archives. After unpacking 146 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB]
Get: 2 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB]
Get: 3 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB]
Get: 4 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB]
Get: 5 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB]
Get: 6 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB]
Get: 7 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB]
Get: 8 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.4-5 [92.4 kB]
Get: 9 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB]
Get: 10 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB]
Get: 11 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB]
Get: 12 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB]
Get: 13 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-3 [862 kB]
Get: 15 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB]
Get: 16 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-1 [24.0 kB]
Get: 17 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2-1 [55.7 kB]
Get: 18 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 19 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-3 [539 kB]
Get: 20 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 22 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 23 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 24 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB]
Get: 25 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get: 26 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB]
Get: 27 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB]
Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b2 [699 kB]
Get: 29 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-1 [1680 kB]
Get: 30 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 31 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 32 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.1 [920 kB]
Get: 33 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-4 [32.8 kB]
Get: 34 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-4 [80.9 kB]
Get: 35 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B]
Get: 36 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-4 [326 kB]
Get: 37 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-4 [138 kB]
Get: 38 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-4 [60.0 kB]
Get: 39 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-4 [42.2 kB]
Get: 40 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-4 [42.4 kB]
Get: 41 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-4 [54.2 kB]
Get: 42 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-4 [126 kB]
Get: 43 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB]
Get: 44 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b7 [316 kB]
Get: 45 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get: 46 http://deb.debian.org/debian unstable/main amd64 libparams-util-perl amd64 1.102-3+b1 [24.4 kB]
Get: 47 http://deb.debian.org/debian unstable/main amd64 libsub-install-perl all 0.929-1 [10.5 kB]
Get: 48 http://deb.debian.org/debian unstable/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB]
Get: 49 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB]
Get: 50 http://deb.debian.org/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get: 51 http://deb.debian.org/debian unstable/main amd64 libconst-fast-perl all 0.014-2 [8792 B]
Get: 52 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB]
Get: 53 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get: 54 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get: 55 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get: 56 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.9-2 [1464 kB]
Get: 57 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8+b1 [19.9 kB]
Get: 58 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8+b1 [57.6 kB]
Get: 59 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.9+dfsg-1 [192 kB]
Get: 60 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB]
Get: 61 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB]
Get: 62 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB]
Get: 63 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB]
Get: 64 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB]
Get: 65 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB]
Get: 66 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB]
Get: 67 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.12.1-3 [365 kB]
Get: 68 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB]
Get: 69 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1+b1 [598 kB]
Get: 70 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.9-2 [455 kB]
Get: 71 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.9-2 [455 kB]
Get: 72 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB]
Get: 73 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-3 [208 kB]
Get: 74 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.20.0-2 [99.2 kB]
Get: 75 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB]
Get: 76 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB]
Get: 77 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10.1-1 [1318 kB]
Get: 78 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.9-2 [1401 kB]
Get: 79 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-4 [15.9 kB]
Get: 80 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.6.9+dfsg-1 [307 kB]
Get: 81 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB]
Get: 82 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB]
Get: 83 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB]
Get: 84 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB]
Get: 85 http://deb.debian.org/debian unstable/main amd64 libnghttp3-dev amd64 1.6.0-2 [88.5 kB]
Get: 86 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls-dev amd64 1.9.1-1 [23.1 kB]
Get: 87 http://deb.debian.org/debian unstable/main amd64 libngtcp2-dev amd64 1.9.1-1 [167 kB]
Get: 88 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB]
Get: 89 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get: 90 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB]
Get: 91 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.4.1-1 [2787 kB]
Get: 92 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB]
Get: 93 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-2 [365 kB]
Get: 94 http://deb.debian.org/debian unstable/main amd64 libcurl4-gnutls-dev amd64 8.12.1-3 [480 kB]
Get: 95 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.23-1+b1 [47.5 kB]
Get: 96 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.23-1+b1 [56.0 kB]
Get: 97 http://deb.debian.org/debian unstable/main amd64 libhtml-tagset-perl all 3.24-1 [14.7 kB]
Get: 98 http://deb.debian.org/debian unstable/main amd64 liburi-perl all 5.30-1 [105 kB]
Get: 99 http://deb.debian.org/debian unstable/main amd64 libhtml-parser-perl amd64 3.83-1+b2 [99.7 kB]
Get: 100 http://deb.debian.org/debian unstable/main amd64 libdevel-cover-perl amd64 1.44-1+b2 [187 kB]
Get: 101 http://deb.debian.org/debian unstable/main amd64 libdevel-symdump-perl all 2.18-5 [15.8 kB]
Get: 102 http://deb.debian.org/debian unstable/main amd64 libfile-slurp-perl all 9999.32-2 [26.7 kB]
Get: 103 http://deb.debian.org/debian unstable/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 104 http://deb.debian.org/debian unstable/main amd64 libhtscodecs2 amd64 1.6.1-2 [95.8 kB]
Get: 105 http://deb.debian.org/debian unstable/main amd64 libhts3t64 amd64 1.21+ds-1 [463 kB]
Get: 106 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB]
Get: 107 http://deb.debian.org/debian unstable/main amd64 libhts-dev amd64 1.21+ds-1 [1733 kB]
Get: 108 http://deb.debian.org/debian unstable/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get: 109 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 110 http://deb.debian.org/debian unstable/main amd64 libpod-parser-perl all 1.67-1 [94.1 kB]
Get: 111 http://deb.debian.org/debian unstable/main amd64 libpod-coverage-perl all 0.23-2 [22.1 kB]
Get: 112 http://deb.debian.org/debian unstable/main amd64 libtry-tiny-perl all 0.32-1 [22.9 kB]
Get: 113 http://deb.debian.org/debian unstable/main amd64 libtest-fatal-perl all 0.017-1 [13.2 kB]
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Processing triggers for libc-bin (2.40-7) ...
Reading package lists...
Building dependency tree...
Reading state information...
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Initializing package states...
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Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/3787794/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for unstable
I: user script /srv/workspace/pbuilder/3787794/tmp/hooks/A99_set_merged_usr finished
hostname: Name or service not known
I: Running cd /build/reproducible-path/allelecount-4.3.0/ && 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  > ../allelecount_4.3.0-3_source.changes
dpkg-buildpackage: info: source package allelecount
dpkg-buildpackage: info: source version 4.3.0-3
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 amd64
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0'
dh_auto_clean --sourcedirectory=c
	cd c && make -j42 clean
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c'
rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c'
dh_auto_clean --sourcedirectory=perl
make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0'
   dh_clean
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0'
dh_auto_configure --sourcedirectory=c
dh_auto_configure --sourcedirectory=perl
	cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LD=x86_64-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now"
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for alleleCount
Writing MYMETA.yml and MYMETA.json
make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0'
   debian/rules override_dh_auto_build
make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0'
dh_auto_build --sourcedirectory=c --no-parallel
	cd c && make -j1 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c'
rm -f ./src/*.o *~ ./bin/alleleCounter ./bin/* ./tests/tests_log ./tests/bam_access_tests ./src/*.gcda ./src/*.gcov ./src/*.gcno *.gcda *.gcov *.gcno ./tests/*.gcda ./tests/*.gcov ./tests/*.gcno
mkdir -p ./bin
mkdir -p ./htslib_tmp
#Do some magic to ensure we compile ALLELECOUNT with the static libhts.a rather than libhts.so
ln -fs /libhts.a ./htslib_tmp/libhts.a
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic -c src/bam_access.c  -o src/bam_access.o
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -I/usr/local//include -Isrc/ -I/ -rdynamic -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -o ./bin/alleleCounter ./src/bam_access.o -L./htslib_tmp -L/usr/local//lib -lhts -lpthread -lz -lbz2 -llzma -lm -ldl ./src/alleleCounter.c -Wl,-z,relro -Wl,-z,now
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic ./src/bam_access.o -L./htslib_tmp -lhts -lpthread -lz -lbz2 -llzma -lm -ldl -L/usr/local//lib -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now  tests/bam_access_tests.c   -o tests/bam_access_tests
tests/bam_access_tests.c: In function ‘test_bam_access_get_position_base_counts’:
tests/bam_access_tests.c:45:13: warning: variable ‘res’ set but not used [-Wunused-but-set-variable]
   45 |         int res = bam_access_get_position_base_counts(chr,pos,stats,0,NULL);
      |             ^~~
sh ./tests/runtests.sh
Running unit tests:
----
RUNNING: ./tests/bam_access_tests
Performing pileup of 11250 reads at 1 198661939
ALL TESTS PASSED
Tests run: 1
tests/bam_access_tests PASS

remove tmp hts location
rm -rf ./htslib_tmp
Binaries have been compiled.
make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c'
dh_auto_build --sourcedirectory=perl
	cd perl && make -j42
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl'
cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.pm
cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm
cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm
cp bin/alleleCounter.pl blib/script/alleleCounter.pl
cp bin/alleleCounterToJson.pl blib/script/alleleCounterToJson.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl
"/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounterToJson.pl
Manifying 2 pod documents
Manifying 2 pod documents
make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0'
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0'
dh_auto_test --sourcedirectory=c
	cd c && make -j42 test
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/c'
sh ./tests/runtests.sh
Running unit tests:
----
RUNNING: ./tests/bam_access_tests
Performing pileup of 11250 reads at 1 198661939
ALL TESTS PASSED
Tests run: 1
tests/bam_access_tests PASS

make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/c'
dh_auto_test --sourcedirectory=perl
	cd perl && make -j42 test TEST_VERBOSE=1
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl'
PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" t/*.t
t/1_pm_compile.t .. 
ok 1 - use Sanger::CGP::AlleleCount;
ok 2 - use Sanger::CGP::AlleleCount::Genotype;
ok 3 - use Sanger::CGP::AlleleCount::ToJson;
ok 4 - Check version inheritance exists (Sanger::CGP::AlleleCount)
ok 5 - Check version inheritance exists (Sanger::CGP::AlleleCount::Genotype)
ok 6 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype'
ok 7 - Check version inheritance exists (Sanger::CGP::AlleleCount::ToJson)
ok 8 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson'
1..8
ok
t/2_pl_compile.t .. 
ok 1 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounter.pl
ok 2 - Compilation check: /build/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.pl
1..2
ok
t/genotype.t ...... 
ok 1 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype'
ok 2 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype'
ok 3 - Check execution of loci profile (BAM)
ok 4 - Expected result for defaults (BAM)
ok 5 - Check execution of loci profile (BAM, pbq=20)
ok 6 - Expected result for defaults (BAM, pbq=20)
ok 7 - Check execution of loci profile (BAM, mapq=1)
ok 8 - Expected result for defaults (BAM, mapq=1)
ok 9 - Check execution of snp6 loci profile (BAM)
ok 10 - Expected result for defaults (BAM)
ok 11 - Check execution of snp6 loci profile (BAM, pbq=20)
ok 12 - Expected result for defaults (BAM, pbq=20)
ok 13 - Check execution of snp6 loci profile (BAM, mapq=1)
ok 14 - Expected result for defaults (BAM, mapq>0)
ok 15 - Check execution of loci profile (CRAM)
ok 16 - Expected result for defaults (CRAM)
ok 17 - Check execution of loci profile (CRAM, pbq=20)
ok 18 - Expected result for defaults (CRAM, pbq=20)
ok 19 - Check execution of loci profile (CRAM, mapq=1)
ok 20 - Expected result for defaults (CRAM, mapq=1)
ok 21 - Check execution of snp6 loci profile (CRAM)
ok 22 - Expected result for defaults (CRAM)
ok 23 - Check execution of snp6 loci profile (CRAM, pbq=20)
ok 24 - Expected result for defaults (CRAM, pbq=20)
ok 25 - Check execution of snp6 loci profile (CRAM, mapq=1)
ok 26 - Expected result for defaults (CRAM, mapq=1)
1..26
ok
t/tojson.t ........ 
ok 1 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson'
ok 2 - Check conversion to JSON
1..2
ok
All tests successful.
Files=4, Tests=38,  3 wallclock secs ( 0.02 usr  0.02 sys +  0.63 cusr  0.11 csys =  0.78 CPU)
Result: PASS
make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_auto_install
make[1]: Entering directory '/build/reproducible-path/allelecount-4.3.0'
dh_auto_install --sourcedirectory=c
dh_auto_install --sourcedirectory=perl
	cd perl && make -j42 install DESTDIR=/build/reproducible-path/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[2]: Entering directory '/build/reproducible-path/allelecount-4.3.0/perl'
Manifying 2 pod documents
Manifying 2 pod documents
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount.pm
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/ToJson.pm
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounterToJson.pl.1p
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl
Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl
make[2]: Leaving directory '/build/reproducible-path/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/reproducible-path/allelecount-4.3.0'
   dh_install
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'allelecount' in '../allelecount_4.3.0-3_amd64.deb'.
dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-3_amd64.deb'.
dpkg-deb: building package 'liballelecount-perl' in '../liballelecount-perl_4.3.0-3_all.deb'.
 dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-3_amd64.buildinfo
 dpkg-genchanges --build=binary -O../allelecount_4.3.0-3_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/3787794/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/3787794/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/3787794 and its subdirectories
I: Current time: Thu Apr  2 15:05:14 +14 2026
I: pbuilder-time-stamp: 1775091914