I: pbuilder: network access will be disabled during build
I: Current time: Fri Apr 21 21:14:50 -12 2023
I: pbuilder-time-stamp: 1682154890
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: 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 Thu Sep 29 23:15:52 2022 -12
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/27841/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='27841'
PS1='# '
PS2='> '
PS4='+ '
PWD='/'
SHELL='/bin/bash'
SHLVL='2'
SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.h9q1U68t/pbuilderrc_ACcm --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.h9q1U68t/b1 --logfile b1/build.log allelecount_4.3.0-2.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink12-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Apr 20 22:25 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/27841/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: arm64
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 ... 19616 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 24.2 MB of archives. After unpacking 92.4 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB]
Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB]
Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 31 http://deb.debian.org/debian bookworm/main arm64 libb-debug-perl all 1.26-3 [11.4 kB]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libparams-util-perl arm64 1.102-2+b1 [24.2 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 libsub-install-perl all 0.929-1 [10.5 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libdata-optlist-perl all 0.113-1 [10.6 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libsub-exporter-perl all 0.989-1 [50.5 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 libconst-fast-perl all 0.014-2 [8792 B]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB]
Get: 43 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB]
Get: 44 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB]
Get: 45 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB]
Get: 46 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB]
Get: 47 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-8 [357 kB]
Get: 48 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-8 [466 kB]
Get: 49 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB]
Get: 50 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB]
Get: 51 http://deb.debian.org/debian bookworm/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 52 http://deb.debian.org/debian bookworm/main arm64 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 53 http://deb.debian.org/debian bookworm/main arm64 liburi-perl all 5.17-1 [90.4 kB]
Get: 54 http://deb.debian.org/debian bookworm/main arm64 libhtml-parser-perl arm64 3.81-1 [98.6 kB]
Get: 55 http://deb.debian.org/debian bookworm/main arm64 libdevel-cover-perl arm64 1.38-1+b1 [192 kB]
Get: 56 http://deb.debian.org/debian bookworm/main arm64 libdevel-symdump-perl all 2.18-5 [15.8 kB]
Get: 57 http://deb.debian.org/debian bookworm/main arm64 libfile-slurp-perl all 9999.32-2 [26.7 kB]
Get: 58 http://deb.debian.org/debian bookworm/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 59 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB]
Get: 60 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB]
Get: 61 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB]
Get: 62 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB]
Get: 63 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB]
Get: 64 http://deb.debian.org/debian bookworm/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB]
Get: 65 http://deb.debian.org/debian bookworm/main arm64 libjson-perl all 4.10000-1 [87.5 kB]
Get: 66 http://deb.debian.org/debian bookworm/main arm64 libpod-parser-perl all 1.65-1 [96.3 kB]
Get: 67 http://deb.debian.org/debian bookworm/main arm64 libpod-coverage-perl all 0.23-2 [22.1 kB]
Get: 68 http://deb.debian.org/debian bookworm/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 69 http://deb.debian.org/debian bookworm/main arm64 libtest-fatal-perl all 0.017-1 [13.2 kB]
Fetched 24.2 MB in 1s (37.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package sensible-utils.
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(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ...
Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ...
Unpacking libmagic-mgc (1:5.44-3) ...
Selecting previously unselected package libmagic1:arm64.
Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ...
Unpacking libmagic1:arm64 (1:5.44-3) ...
Selecting previously unselected package file.
Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ...
Unpacking file (1:5.44-3) ...
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Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ...
Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.7-1) ...
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Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ...
Unpacking groff-base (1.22.4-10) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ...
Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.7-1) ...
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Unpacking man-db (2.11.2-2) ...
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Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ...
Unpacking m4 (1.4.19-3) ...
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Preparing to unpack .../11-autoconf_2.71-3_all.deb ...
Unpacking autoconf (2.71-3) ...
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Unpacking autotools-dev (20220109.1) ...
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Unpacking libdebhelper-perl (13.11.4) ...
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Unpacking libtool (2.4.7-5) ...
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Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
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Unpacking libsub-override-perl (0.09-4) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
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Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ...
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Unpacking dh-strip-nondeterminism (1.13.1-1) ...
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Unpacking libelf1:arm64 (0.188-2.1) ...
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Unpacking dwz (0.15-1) ...
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Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ...
Unpacking libicu72:arm64 (72.1-3) ...
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Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ...
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Unpacking gettext (0.21-12) ...
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Unpacking intltool-debian (0.35.0+20060710.6) ...
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Selecting previously unselected package libparams-util-perl.
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Unpacking libparams-util-perl (1.102-2+b1) ...
Selecting previously unselected package libsub-install-perl.
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/allelecount-4.3.0/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 arm64
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/allelecount-4.3.0'
dh_auto_clean --sourcedirectory=c
cd c && make -j8 clean
make[2]: Entering directory '/build/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/allelecount-4.3.0/c'
dh_auto_clean --sourcedirectory=perl
make[1]: Leaving directory '/build/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/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 -ffile-prefix-map=/build/allelecount-4.3.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-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]: Leaving directory '/build/allelecount-4.3.0'
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/allelecount-4.3.0'
dh_auto_build --sourcedirectory=c
cd c && make -j8 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/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 -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]: Leaving directory '/build/allelecount-4.3.0/c'
dh_auto_build --sourcedirectory=perl
cd perl && make -j8
make[2]: Entering directory '/build/allelecount-4.3.0/perl'
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]: Leaving directory '/build/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/allelecount-4.3.0'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/allelecount-4.3.0'
dh_auto_test --sourcedirectory=c
cd c && make -j8 test
make[2]: Entering directory '/build/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/allelecount-4.3.0/c'
dh_auto_test --sourcedirectory=perl
cd perl && make -j8 test TEST_VERBOSE=1
make[2]: Entering directory '/build/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::ToJson;
ok 3 - use Sanger::CGP::AlleleCount::Genotype;
ok 4 - Check version inheritance exists (Sanger::CGP::AlleleCount)
ok 5 - Check version inheritance exists (Sanger::CGP::AlleleCount::ToJson)
ok 6 - An object of class 'Sanger::CGP::AlleleCount::ToJson' isa 'Sanger::CGP::AlleleCount::ToJson'
ok 7 - Check version inheritance exists (Sanger::CGP::AlleleCount::Genotype)
ok 8 - An object of class 'Sanger::CGP::AlleleCount::Genotype' isa 'Sanger::CGP::AlleleCount::Genotype'
1..8
ok
t/2_pl_compile.t ..
ok 1 - Compilation check: /build/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.pl
ok 2 - Compilation check: /build/allelecount-4.3.0/perl/t/../bin/alleleCounter.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 ( 0.07 usr 0.02 sys + 2.22 cusr 0.33 csys = 2.64 CPU)
Result: PASS
make[2]: Leaving directory '/build/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/allelecount-4.3.0'
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/allelecount-4.3.0'
dh_auto_install --sourcedirectory=c
dh_auto_install --sourcedirectory=perl
cd perl && make -j8 install DESTDIR=/build/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr
make[2]: Entering directory '/build/allelecount-4.3.0/perl'
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/alleleCounterToJson.pl.1p
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/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/alleleCounterToJson.pl
Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.pl
make[2]: Leaving directory '/build/allelecount-4.3.0/perl'
make[1]: Leaving directory '/build/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 'liballelecount-perl' in '../liballelecount-perl_4.3.0-2_all.deb'.
dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-2_arm64.deb'.
dpkg-deb: building package 'allelecount' in '../allelecount_4.3.0-2_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-2_arm64.buildinfo
dpkg-genchanges --build=binary -O../allelecount_4.3.0-2_arm64.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: 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/27841 and its subdirectories
I: Current time: Fri Apr 21 21:16:02 -12 2023
I: pbuilder-time-stamp: 1682154962