I: pbuilder: network access will be disabled during build
I: Current time: Wed Jun 12 17:59:34 +14 2024
I: pbuilder-time-stamp: 1718164774
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-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 [allelecount_4.3.0-2.dsc]
I: copying [./allelecount_4.3.0.orig.tar.gz]
I: copying [./allelecount_4.3.0-2.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Oct 1 01:15:52 2022 +14
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./allelecount_4.3.0-2.dsc: no acceptable signature found
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_4.3.0-2.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/79616/tmp/hooks/D01_modify_environment starting
debug: Running on ionos6-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 Jun 12 17:59 /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/79616/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/79616/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]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
BASH_VERSION='5.2.15(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=i386
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15'
DIRSTACK=()
DISTRIBUTION=bookworm
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=i686
HOST_ARCH=i386
IFS='
'
INVOCATION_ID=1b573c84bd15493fad9006a08e523e35
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=79616
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.P0tmGNca/pbuilderrc_LSet --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.P0tmGNca/b2 --logfile b2/build.log --extrapackages usrmerge allelecount_4.3.0-2.dsc'
SUDO_GID=112
SUDO_UID=107
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://85.184.249.68:3128
I: uname -a
Linux i-capture-the-hostname 5.10.0-22-amd64 #1 SMP Debian 5.10.178-3 (2023-04-22) x86_64 GNU/Linux
I: ls -l /bin
total 6036
-rwxr-xr-x 1 root root 1408088 Apr 24 2023 bash
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep
-rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2
-rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover
lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore
-rwxr-xr-x 1 root root 42920 Sep 21 2022 cat
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chgrp
-rwxr-xr-x 1 root root 67496 Sep 21 2022 chmod
-rwxr-xr-x 1 root root 79816 Sep 21 2022 chown
-rwxr-xr-x 1 root root 162024 Sep 21 2022 cp
-rwxr-xr-x 1 root root 136916 Jan 6 2023 dash
-rwxr-xr-x 1 root root 137160 Sep 21 2022 date
-rwxr-xr-x 1 root root 100364 Sep 21 2022 dd
-rwxr-xr-x 1 root root 108940 Sep 21 2022 df
-rwxr-xr-x 1 root root 162152 Sep 21 2022 dir
-rwxr-xr-x 1 root root 87760 Mar 24 2023 dmesg
lrwxrwxrwx 1 root root 8 Dec 20 2022 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Dec 20 2022 domainname -> hostname
-rwxr-xr-x 1 root root 38760 Sep 21 2022 echo
-rwxr-xr-x 1 root root 41 Jan 25 2023 egrep
-rwxr-xr-x 1 root root 34664 Sep 21 2022 false
-rwxr-xr-x 1 root root 41 Jan 25 2023 fgrep
-rwxr-xr-x 1 root root 84272 Mar 24 2023 findmnt
-rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount
-rwxr-xr-x 1 root root 218680 Jan 25 2023 grep
-rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip
-rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe
-rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip
-rwxr-xr-x 1 root root 21916 Dec 20 2022 hostname
-rwxr-xr-x 1 root root 75756 Sep 21 2022 ln
-rwxr-xr-x 1 root root 55600 Mar 24 2023 login
-rwxr-xr-x 1 root root 162152 Sep 21 2022 ls
-rwxr-xr-x 1 root root 214568 Mar 24 2023 lsblk
-rwxr-xr-x 1 root root 96328 Sep 21 2022 mkdir
-rwxr-xr-x 1 root root 84008 Sep 21 2022 mknod
-rwxr-xr-x 1 root root 38792 Sep 21 2022 mktemp
-rwxr-xr-x 1 root root 63016 Mar 24 2023 more
-rwsr-xr-x 1 root root 58912 Mar 24 2023 mount
-rwxr-xr-x 1 root root 13856 Mar 24 2023 mountpoint
-rwxr-xr-x 1 root root 157932 Sep 21 2022 mv
lrwxrwxrwx 1 root root 8 Dec 20 2022 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 38792 Sep 21 2022 pwd
lrwxrwxrwx 1 root root 4 Apr 24 2023 rbash -> bash
-rwxr-xr-x 1 root root 51080 Sep 21 2022 readlink
-rwxr-xr-x 1 root root 75720 Sep 21 2022 rm
-rwxr-xr-x 1 root root 51080 Sep 21 2022 rmdir
-rwxr-xr-x 1 root root 22308 Nov 3 2022 run-parts
-rwxr-xr-x 1 root root 133224 Jan 6 2023 sed
lrwxrwxrwx 1 root root 9 Jun 12 17:59 sh -> /bin/bash
-rwxr-xr-x 1 root root 38760 Sep 21 2022 sleep
-rwxr-xr-x 1 root root 87976 Sep 21 2022 stty
-rwsr-xr-x 1 root root 83492 Mar 24 2023 su
-rwxr-xr-x 1 root root 38792 Sep 21 2022 sync
-rwxr-xr-x 1 root root 598456 Apr 7 2023 tar
-rwxr-xr-x 1 root root 13860 Nov 3 2022 tempfile
-rwxr-xr-x 1 root root 120776 Sep 21 2022 touch
-rwxr-xr-x 1 root root 34664 Sep 21 2022 true
-rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server
-rwsr-xr-x 1 root root 30236 Mar 24 2023 umount
-rwxr-xr-x 1 root root 38760 Sep 21 2022 uname
-rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress
-rwxr-xr-x 1 root root 162152 Sep 21 2022 vdir
-rwxr-xr-x 1 root root 71216 Mar 24 2023 wdctl
lrwxrwxrwx 1 root root 8 Dec 20 2022 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat
-rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp
-rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff
-rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep
-rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep
-rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce
-rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep
-rwxr-xr-x 1 root root 2206 Apr 10 2022 zless
-rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore
-rwxr-xr-x 1 root root 4577 Apr 10 2022 znew
I: user script /srv/workspace/pbuilder/79616/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), 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 ... 19604 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} 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} libb-debug-perl{a} libbrotli1{a} libbz2-dev{a} libconst-fast-perl{a} libcurl3-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} libelf1{a} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libipc-system-simple-perl{a} libjson-perl{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libparams-util-perl{a} libpipeline1{a} libpod-coverage-perl{a} libpod-parser-perl{a} libpsl5{a} libregexp-ipv6-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-perl{a} libsub-override-perl{a} libtest-fatal-perl{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} liburi-perl{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libhttp-message-perl libjson-xs-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtemplate-perl lynx publicsuffix wget
0 packages upgraded, 69 newly installed, 0 to remove and 0 not upgraded.
Need to get 25.2 MB of archives. After unpacking 88.8 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB]
Get: 4 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB]
Get: 6 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB]
Get: 8 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB]
Get: 9 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB]
Get: 10 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB]
Get: 11 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB]
Get: 12 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB]
Get: 24 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB]
Get: 25 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB]
Get: 26 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.2 [720 kB]
Get: 27 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB]
Get: 28 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main i386 libb-debug-perl all 1.26-3 [11.4 kB]
Get: 32 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB]
Get: 33 http://deb.debian.org/debian bookworm/main i386 libbz2-dev i386 1.0.8-5+b1 [31.5 kB]
Get: 34 http://deb.debian.org/debian bookworm/main i386 libparams-util-perl i386 1.102-2+b1 [25.0 kB]
Get: 35 http://deb.debian.org/debian bookworm/main i386 libsub-install-perl all 0.929-1 [10.5 kB]
Get: 36 http://deb.debian.org/debian bookworm/main i386 libdata-optlist-perl all 0.113-1 [10.6 kB]
Get: 37 http://deb.debian.org/debian bookworm/main i386 libsub-exporter-perl all 0.989-1 [50.5 kB]
Get: 38 http://deb.debian.org/debian bookworm/main i386 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get: 39 http://deb.debian.org/debian bookworm/main i386 libconst-fast-perl all 0.014-2 [8792 B]
Get: 40 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB]
Get: 41 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB]
Get: 42 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB]
Get: 43 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1 [79.8 kB]
Get: 44 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB]
Get: 45 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB]
Get: 46 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB]
Get: 47 http://deb.debian.org/debian bookworm/main i386 libcurl3-gnutls i386 7.88.1-9 [412 kB]
Get: 48 http://deb.debian.org/debian bookworm/main i386 libcurl4-gnutls-dev i386 7.88.1-9 [527 kB]
Get: 49 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB]
Get: 50 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB]
Get: 51 http://deb.debian.org/debian bookworm/main i386 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 52 http://deb.debian.org/debian bookworm/main i386 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 53 http://deb.debian.org/debian bookworm/main i386 liburi-perl all 5.17-1 [90.4 kB]
Get: 54 http://deb.debian.org/debian bookworm/main i386 libhtml-parser-perl i386 3.81-1 [102 kB]
Get: 55 http://deb.debian.org/debian bookworm/main i386 libdevel-cover-perl i386 1.38-1+b1 [194 kB]
Get: 56 http://deb.debian.org/debian bookworm/main i386 libdevel-symdump-perl all 2.18-5 [15.8 kB]
Get: 57 http://deb.debian.org/debian bookworm/main i386 libfile-slurp-perl all 9999.32-2 [26.7 kB]
Get: 58 http://deb.debian.org/debian bookworm/main i386 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 59 http://deb.debian.org/debian bookworm/main i386 libhtscodecs2 i386 1.3.0-4 [67.4 kB]
Get: 60 http://deb.debian.org/debian bookworm/main i386 libhts3 i386 1.16+ds-3 [469 kB]
Get: 61 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB]
Get: 62 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB]
Get: 63 http://deb.debian.org/debian bookworm/main i386 libhts-dev i386 1.16+ds-3 [1585 kB]
Get: 64 http://deb.debian.org/debian bookworm/main i386 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get: 65 http://deb.debian.org/debian bookworm/main i386 libjson-perl all 4.10000-1 [87.5 kB]
Get: 66 http://deb.debian.org/debian bookworm/main i386 libpod-parser-perl all 1.65-1 [96.3 kB]
Get: 67 http://deb.debian.org/debian bookworm/main i386 libpod-coverage-perl all 0.23-2 [22.1 kB]
Get: 68 http://deb.debian.org/debian bookworm/main i386 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 69 http://deb.debian.org/debian bookworm/main i386 libtest-fatal-perl all 0.017-1 [13.2 kB]
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I: Building the package
I: user script /srv/workspace/pbuilder/79616/tmp/hooks/A99_set_merged_usr starting
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I: Running cd /build/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_4.3.0-2_source.changes
dpkg-buildpackage: info: source package allelecount
dpkg-buildpackage: info: source version 4.3.0-2
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]: Verzeichnis „/build/allelecount-4.3.0“ wird betreten
dh_auto_clean --sourcedirectory=c
cd c && make -j15 clean
make[2]: Verzeichnis „/build/allelecount-4.3.0/c“ wird betreten
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]: Verzeichnis „/build/allelecount-4.3.0/c“ wird verlassen
dh_auto_clean --sourcedirectory=perl
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird verlassen
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
debian/rules override_dh_auto_configure
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird betreten
dh_auto_configure --sourcedirectory=c
dh_auto_configure --sourcedirectory=perl
cd perl && /usr/bin/perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=i686-linux-gnu-gcc -g -O2 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -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]: Verzeichnis „/build/allelecount-4.3.0“ wird verlassen
debian/rules override_dh_auto_build
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird betreten
dh_auto_build --sourcedirectory=c
cd c && make -j15 "INSTALL=install --strip-program=true"
make[2]: Verzeichnis „/build/allelecount-4.3.0/c“ wird betreten
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 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -I/usr/local//include -Isrc/ -I/ -rdynamic -c src/bam_access.c -o src/bam_access.o
src/bam_access.c: In function ‘pileupCounts’:
src/bam_access.c:132:70: warning: ‘pre_b’ may be used uninitialized [-Wmaybe-uninitialized]
132 | if(!(p->is_del) && qual >= min_base_qual && (absent || pre_b != c)){
| ~~~~~~~~^~~~~~~~~~~~~~
src/bam_access.c:124:25: note: ‘pre_b’ was declared here
124 | uint8_t pre_b;
| ^~~~~
gcc -O3 -DALLELECOUNTER_VERSION='"4.3.0"' -I/usr/local//include -Isrc/ -I/ -rdynamic -g -O2 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -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 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -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]: Verzeichnis „/build/allelecount-4.3.0/c“ wird verlassen
dh_auto_build --sourcedirectory=perl
cd perl && make -j15
make[2]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird betreten
cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm
cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.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]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird verlassen
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird verlassen
debian/rules override_dh_auto_test
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird betreten
dh_auto_test --sourcedirectory=c
cd c && make -j15 test
make[2]: Verzeichnis „/build/allelecount-4.3.0/c“ wird betreten
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]: Verzeichnis „/build/allelecount-4.3.0/c“ wird verlassen
dh_auto_test --sourcedirectory=perl
cd perl && make -j15 test TEST_VERBOSE=1
make[2]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird betreten
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/allelecount-4.3.0/perl/t/../bin/alleleCounter.pl
ok 2 - Compilation check: /build/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, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.60 cusr 0.06 csys = 0.68 CPU)
Result: PASS
make[2]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird verlassen
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird verlassen
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird betreten
dh_auto_install --sourcedirectory=c
dh_auto_install --sourcedirectory=perl
cd perl && make -j15 install DESTDIR=/build/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[2]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird betreten
Manifying 2 pod documents
Manifying 2 pod documents
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount.pm
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/Genotype.pm
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/perl5/Sanger/CGP/AlleleCount/ToJson.pm
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounter.pl.1p
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man1/alleleCounterToJson.pl.1p
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::ToJson.3pm
Installing /build/allelecount-4.3.0/debian/tmp/usr/share/man/man3/Sanger::CGP::AlleleCount::Genotype.3pm
Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl
Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl
make[2]: Verzeichnis „/build/allelecount-4.3.0/perl“ wird verlassen
make[1]: Verzeichnis „/build/allelecount-4.3.0“ wird verlassen
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: Paket »allelecount« wird in »../allelecount_4.3.0-2_i386.deb« gebaut.
dpkg-deb: Paket »allelecount-dbgsym« wird in »../allelecount-dbgsym_4.3.0-2_i386.deb« gebaut.
dpkg-deb: Paket »liballelecount-perl« wird in »../liballelecount-perl_4.3.0-2_all.deb« gebaut.
dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-2_i386.buildinfo
dpkg-genchanges --build=binary -O../allelecount_4.3.0-2_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/79616/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/79616/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/79616 and its subdirectories
I: Current time: Wed Jun 12 18:00:07 +14 2024
I: pbuilder-time-stamp: 1718164807