I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 25 07:23:39 +14 2025 I: pbuilder-time-stamp: 1750785819 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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 Fri Sep 30 11:15:52 2022 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/2649445/tmp/hooks/D01_modify_environment starting debug: Running on codethink01-arm64. 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 24 17:23 /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/2649445/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2649445/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]="21" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.21(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=13f13df6cd454a90950e66c337a7c5dc LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-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=2649445 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.VQ8rR0fz/pbuilderrc_pDPy --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.VQ8rR0fz/b2 --logfile b2/build.log allelecount_4.3.0-2.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-21-cloud-arm64 #1 SMP Debian 6.1.90-1 (2024-05-03) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 22 17:48 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2649445/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 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 ... 19746 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} 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} libfile-slurp-perl{a} libfile-stripnondeterminism-perl{a} libfile-which-perl{a} libgssapi-krb5-2{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libipc-system-simple-perl{a} libjson-perl{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libparams-util-perl{a} libpipeline1{a} libpod-coverage-perl{a} libpod-parser-perl{a} libpsl5t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libsub-exporter-perl{a} libsub-exporter-progressive-perl{a} libsub-install-perl{a} libsub-override-perl{a} libsub-prototype-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 krb5-locales 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, 74 newly installed, 0 to remove and 0 not upgraded. Need to get 25.4 MB of archives. After unpacking 97.5 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40.1-1 [93.2 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 libparams-util-perl arm64 1.102-3 [23.4 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 libsub-prototype-perl arm64 0.03-2+b2 [9776 B] Get: 25 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.11-1 [10.4 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 28 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 37 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 40 http://deb.debian.org/debian trixie/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get: 41 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 44 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 52 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-5 [405 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-5 [524 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libhtml-tagset-perl all 3.24-1 [14.7 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 liburi-perl all 5.28-1 [98.6 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 libhtml-parser-perl arm64 3.82-1 [96.9 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libdevel-cover-perl arm64 1.42-1 [184 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libdevel-symdump-perl all 2.18-5 [15.8 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1 [916 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 libjson-perl all 4.10000-1 [87.5 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libpod-parser-perl all 1.67-1 [94.1 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libtest-fatal-perl all 0.017-1 [13.2 kB] Fetched 25.4 MB in 0s (53.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19746 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40.1-1_arm64.deb ... Unpacking bsdextrautils (2.40.1-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... 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Adding 'diversion of /usr/bin/podselect to /usr/bin/podselect.bundled by libpod-parser-perl' Adding 'diversion of /usr/share/man/man1/podselect.1.gz to /usr/share/man/man1/podselect.bundled.1.gz by libpod-parser-perl' Unpacking libpod-parser-perl (1.67-1) ... Selecting previously unselected package libpod-coverage-perl. Preparing to unpack .../71-libpod-coverage-perl_0.23-2_all.deb ... Unpacking libpod-coverage-perl (0.23-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../72-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libtest-fatal-perl. Preparing to unpack .../73-libtest-fatal-perl_0.017-1_all.deb ... Unpacking libtest-fatal-perl (0.017-1) ... Setting up libhtscodecs2:arm64 (1.6.0-1+b1) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libfile-which-perl (1.27-2) ... Setting up libkeyutils1:arm64 (1.6.3-3) ... Setting up libfile-slurp-perl (9999.32-2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2649445/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/2649445/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_4.3.0-2_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 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/reproducible-path/allelecount-4.3.0' dh_auto_clean --sourcedirectory=c cd c && make -j12 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 -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2" "LD=aarch64-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 -mbranch-protection=standard -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 cd c && make -j12 "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 -mbranch-protection=standard -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 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/allelecount-4.3.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 -mbranch-protection=standard -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 -j12 make[2]: Entering directory '/build/reproducible-path/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 "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/alleleCounter.pl cp bin/alleleCounterToJson.pl blib/script/alleleCounterToJson.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 -j12 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 -j12 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::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/reproducible-path/allelecount-4.3.0/perl/t/../bin/alleleCounterToJson.pl ok 2 - Compilation check: /build/reproducible-path/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, 1 wallclock secs ( 0.02 usr 0.00 sys + 0.52 cusr 0.13 csys = 0.67 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 -j12 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/alleleCounterToJson.pl Installing /build/reproducible-path/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounter.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_4.3.0-2_arm64.deb'. dpkg-deb: building package 'allelecount-dbgsym' in '../allelecount-dbgsym_4.3.0-2_arm64.deb'. dpkg-deb: building package 'liballelecount-perl' in '../liballelecount-perl_4.3.0-2_all.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: user script /srv/workspace/pbuilder/2649445/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2649445/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/2649445 and its subdirectories I: Current time: Wed Jun 25 07:24:48 +14 2025 I: pbuilder-time-stamp: 1750785888