I: pbuilder: network access will be disabled during build I: Current time: Mon May 22 17:50:20 +14 2023 I: pbuilder-time-stamp: 1684727420 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 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/9235/tmp/hooks/D01_modify_environment starting debug: Running on cbxi4a. 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 May 22 17:51 /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/9235/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/9235/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]="arm-unknown-linux-gnueabihf") 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=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=e86941d51bdb4ac8b2b673d519517125 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf 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=9235 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.i6iyqw9c/pbuilderrc_RMwh --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.i6iyqw9c/b2 --logfile b2/build.log --extrapackages usrmerge allelecount_4.3.0-2.dsc' SUDO_GID=113 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:3142/ I: uname -a Linux i-capture-the-hostname 5.10.0-23-armmp #1 SMP Debian 5.10.179-1 (2023-05-12) armv7l GNU/Linux I: ls -l /bin total 5072 -rwxr-xr-x 1 root root 838488 Apr 24 11:24 bash -rwxr-xr-x 3 root root 67144 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 67144 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 67144 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 67112 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 67632 Sep 21 2022 cat -rwxr-xr-x 1 root root 67676 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 67644 Sep 21 2022 chmod -rwxr-xr-x 1 root root 67684 Sep 21 2022 chown -rwxr-xr-x 1 root root 133532 Sep 21 2022 cp -rwxr-xr-x 1 root root 132868 Jan 6 03:20 dash -rwxr-xr-x 1 root root 133220 Sep 21 2022 date -rwxr-xr-x 1 root root 67732 Sep 21 2022 dd -rwxr-xr-x 1 root root 68104 Sep 21 2022 df -rwxr-xr-x 1 root root 133632 Sep 21 2022 dir -rwxr-xr-x 1 root root 59128 Mar 23 23:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 67560 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 67548 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 55748 Mar 23 23:02 findmnt -rwsr-xr-x 1 root root 26208 Mar 23 22:15 fusermount -rwxr-xr-x 1 root root 128608 Jan 25 04:43 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 64220 Apr 10 2022 gzip -rwxr-xr-x 1 root root 67032 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 67720 Sep 21 2022 ln -rwxr-xr-x 1 root root 35132 Mar 23 23:51 login -rwxr-xr-x 1 root root 133632 Sep 21 2022 ls -rwxr-xr-x 1 root root 136808 Mar 23 23:02 lsblk -rwxr-xr-x 1 root root 67800 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 67764 Sep 21 2022 mknod -rwxr-xr-x 1 root root 67596 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 38504 Mar 23 23:02 more -rwsr-xr-x 1 root root 38496 Mar 23 23:02 mount -rwxr-xr-x 1 root root 9824 Mar 23 23:02 mountpoint -rwxr-xr-x 1 root root 133532 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 67608 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:24 rbash -> bash -rwxr-xr-x 1 root root 67600 Sep 21 2022 readlink -rwxr-xr-x 1 root root 67672 Sep 21 2022 rm -rwxr-xr-x 1 root root 67600 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 67400 Nov 3 2022 run-parts -rwxr-xr-x 1 root root 133372 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 May 22 17:51 sh -> /bin/bash -rwxr-xr-x 1 root root 67584 Sep 21 2022 sleep -rwxr-xr-x 1 root root 67644 Sep 21 2022 stty -rwsr-xr-x 1 root root 50800 Mar 23 23:02 su -rwxr-xr-x 1 root root 67584 Sep 21 2022 sync -rwxr-xr-x 1 root root 336764 Apr 7 04:25 tar -rwxr-xr-x 1 root root 67144 Nov 3 2022 tempfile -rwxr-xr-x 1 root root 133224 Sep 21 2022 touch -rwxr-xr-x 1 root root 67548 Sep 21 2022 true -rwxr-xr-x 1 root root 9768 Mar 23 22:15 ulockmgr_server -rwsr-xr-x 1 root root 22108 Mar 23 23:02 umount -rwxr-xr-x 1 root root 67572 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 133632 Sep 21 2022 vdir -rwxr-xr-x 1 root root 42608 Mar 23 23:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 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/9235/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: armhf 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 ... 19329 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 23.8 MB of archives. After unpacking 81.7 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main armhf sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main armhf libmagic-mgc armhf 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main armhf libmagic1 armhf 1:5.44-3 [96.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main armhf file armhf 1:5.44-3 [41.6 kB] Get: 5 http://deb.debian.org/debian bookworm/main armhf gettext-base armhf 0.21-12 [157 kB] Get: 6 http://deb.debian.org/debian bookworm/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main armhf groff-base armhf 1.22.4-10 [825 kB] Get: 8 http://deb.debian.org/debian bookworm/main armhf bsdextrautils armhf 2.38.1-5+b1 [78.6 kB] Get: 9 http://deb.debian.org/debian bookworm/main armhf libpipeline1 armhf 1.5.7-1 [33.6 kB] Get: 10 http://deb.debian.org/debian bookworm/main armhf man-db armhf 2.11.2-2 [1351 kB] Get: 11 http://deb.debian.org/debian bookworm/main armhf m4 armhf 1.4.19-3 [265 kB] Get: 12 http://deb.debian.org/debian bookworm/main armhf autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main armhf autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main armhf libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main armhf libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main armhf dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main armhf libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main armhf libelf1 armhf 0.188-2.1 [170 kB] Get: 24 http://deb.debian.org/debian bookworm/main armhf dwz armhf 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main armhf libicu72 armhf 72.1-3 [9048 kB] Get: 26 http://deb.debian.org/debian bookworm/main armhf libxml2 armhf 2.9.14+dfsg-1.2 [591 kB] Get: 27 http://deb.debian.org/debian bookworm/main armhf gettext armhf 0.21-12 [1229 kB] Get: 28 http://deb.debian.org/debian bookworm/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main armhf debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main armhf libb-debug-perl all 1.26-3 [11.4 kB] Get: 32 http://deb.debian.org/debian bookworm/main armhf libbrotli1 armhf 1.0.9-2+b6 [271 kB] Get: 33 http://deb.debian.org/debian bookworm/main armhf libbz2-dev armhf 1.0.8-5+b1 [28.1 kB] Get: 34 http://deb.debian.org/debian bookworm/main armhf libparams-util-perl armhf 1.102-2+b1 [23.8 kB] Get: 35 http://deb.debian.org/debian bookworm/main armhf libsub-install-perl all 0.929-1 [10.5 kB] Get: 36 http://deb.debian.org/debian bookworm/main armhf libdata-optlist-perl all 0.113-1 [10.6 kB] Get: 37 http://deb.debian.org/debian bookworm/main armhf libsub-exporter-perl all 0.989-1 [50.5 kB] Get: 38 http://deb.debian.org/debian bookworm/main armhf libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get: 39 http://deb.debian.org/debian bookworm/main armhf libconst-fast-perl all 0.014-2 [8792 B] Get: 40 http://deb.debian.org/debian bookworm/main armhf libsasl2-modules-db armhf 2.1.28+dfsg-10 [19.0 kB] Get: 41 http://deb.debian.org/debian bookworm/main armhf libsasl2-2 armhf 2.1.28+dfsg-10 [52.3 kB] Get: 42 http://deb.debian.org/debian bookworm/main armhf libldap-2.5-0 armhf 2.5.13+dfsg-5 [158 kB] Get: 43 http://deb.debian.org/debian bookworm/main armhf libnghttp2-14 armhf 1.52.0-1 [60.8 kB] Get: 44 http://deb.debian.org/debian bookworm/main armhf libpsl5 armhf 0.21.2-1 [57.5 kB] Get: 45 http://deb.debian.org/debian bookworm/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB] Get: 46 http://deb.debian.org/debian bookworm/main armhf libssh2-1 armhf 1.10.0-3+b1 [163 kB] Get: 47 http://deb.debian.org/debian bookworm/main armhf libcurl3-gnutls armhf 7.88.1-9 [343 kB] Get: 48 http://deb.debian.org/debian bookworm/main armhf libcurl4-gnutls-dev armhf 7.88.1-9 [448 kB] Get: 49 http://deb.debian.org/debian bookworm/main armhf libdeflate0 armhf 1.14-1 [52.2 kB] Get: 50 http://deb.debian.org/debian bookworm/main armhf libdeflate-dev armhf 1.14-1 [48.7 kB] Get: 51 http://deb.debian.org/debian bookworm/main armhf libhtml-tagset-perl all 3.20-6 [11.7 kB] Get: 52 http://deb.debian.org/debian bookworm/main armhf libregexp-ipv6-perl all 0.03-3 [5212 B] Get: 53 http://deb.debian.org/debian bookworm/main armhf liburi-perl all 5.17-1 [90.4 kB] Get: 54 http://deb.debian.org/debian bookworm/main armhf libhtml-parser-perl armhf 3.81-1 [97.4 kB] Get: 55 http://deb.debian.org/debian bookworm/main armhf libdevel-cover-perl armhf 1.38-1+b1 [191 kB] Get: 56 http://deb.debian.org/debian bookworm/main armhf libdevel-symdump-perl all 2.18-5 [15.8 kB] Get: 57 http://deb.debian.org/debian bookworm/main armhf libfile-slurp-perl all 9999.32-2 [26.7 kB] Get: 58 http://deb.debian.org/debian bookworm/main armhf libfile-which-perl all 1.27-2 [15.1 kB] Get: 59 http://deb.debian.org/debian bookworm/main armhf libhtscodecs2 armhf 1.3.0-4 [60.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main armhf libhts3 armhf 1.16+ds-3 [375 kB] Get: 61 http://deb.debian.org/debian bookworm/main armhf liblzma-dev armhf 5.4.1-0.2 [248 kB] Get: 62 http://deb.debian.org/debian bookworm/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-1 [902 kB] Get: 63 http://deb.debian.org/debian bookworm/main armhf libhts-dev armhf 1.16+ds-3 [1517 kB] Get: 64 http://deb.debian.org/debian bookworm/main armhf libipc-system-simple-perl all 1.30-2 [26.8 kB] Get: 65 http://deb.debian.org/debian bookworm/main armhf libjson-perl all 4.10000-1 [87.5 kB] Get: 66 http://deb.debian.org/debian bookworm/main armhf libpod-parser-perl all 1.65-1 [96.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main armhf libpod-coverage-perl all 0.23-2 [22.1 kB] Get: 68 http://deb.debian.org/debian bookworm/main armhf libtry-tiny-perl all 0.31-2 [22.6 kB] Get: 69 http://deb.debian.org/debian bookworm/main armhf libtest-fatal-perl all 0.017-1 [13.2 kB] Fetched 23.8 MB in 3s (7920 kB/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 ... 19329 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_armhf.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:armhf. Preparing to unpack .../02-libmagic1_1%3a5.44-3_armhf.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 (1.65-1) ... Selecting previously unselected package libpod-coverage-perl. Preparing to unpack .../66-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 .../67-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 .../68-libtest-fatal-perl_0.017-1_all.deb ... Unpacking libtest-fatal-perl (0.017-1) ... Setting up libhtscodecs2:armhf (1.3.0-4) ... Setting up libpipeline1:armhf (1.5.7-1) ... Setting up libfile-which-perl (1.27-2) ... Setting up libpsl5:armhf (0.21.2-1) ... Setting up libfile-slurp-perl (9999.32-2) ... Setting up libicu72:armhf (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:armhf (1.0.9-2+b6) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libnghttp2-14:armhf (1.52.0-1) ... Setting up libmagic1:armhf (1:5.44-3) ... Setting up libtest-fatal-perl (0.017-1) ... Setting up libdeflate0:armhf (1.14-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libb-debug-perl (1.26-3) ... Setting up libsub-install-perl (0.929-1) ... Setting up libsasl2-modules-db:armhf (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libpod-parser-perl (1.65-1) ... Setting up autopoint (0.21-12) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libsasl2-2:armhf (2.1.28+dfsg-10) ... Setting up autoconf (2.71-3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up liblzma-dev:armhf (5.4.1-0.2) ... Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:armhf (0.0.7-1) ... Setting up libjson-perl (4.10000-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:armhf (1.10.0-3+b1) ... Setting up libdevel-symdump-perl (2.18-5) ... Setting up libdeflate-dev:armhf (1.14-1) ... Setting up libelf1:armhf (0.188-2.1) ... Setting up libxml2:armhf (2.9.14+dfsg-1.2) ... Setting up liburi-perl (5.17-1) ... Setting up libbz2-dev:armhf (1.0.8-5+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libtool (2.4.7-5) ... Setting up libpod-coverage-perl (0.23-2) ... Setting up libldap-2.5-0:armhf (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libdata-optlist-perl (0.113-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libhtml-parser-perl:armhf (3.81-1) ... Setting up libsub-exporter-perl (0.989-1) ... Setting up libdevel-cover-perl (1.38-1+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.88.1-9) ... Setting up libcurl4-gnutls-dev:armhf (7.88.1-9) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libconst-fast-perl (0.014-2) ... Setting up libhts3:armhf (1.16+ds-3) ... Setting up libhts-dev:armhf (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-9) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/9235/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/9235/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known 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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: ingresso nella directory «/build/allelecount-4.3.0» dh_auto_clean --sourcedirectory=c cd c && make -j4 clean make[2]: ingresso nella 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]: uscita dalla directory «/build/allelecount-4.3.0/c» dh_auto_clean --sourcedirectory=perl make[1]: uscita dalla 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]: ingresso nella 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=arm-linux-gnueabihf-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]: uscita dalla directory «/build/allelecount-4.3.0» debian/rules override_dh_auto_build make[1]: ingresso nella directory «/build/allelecount-4.3.0» dh_auto_build --sourcedirectory=c cd c && make -j4 "INSTALL=install --strip-program=true" make[2]: ingresso nella 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]: uscita dalla directory «/build/allelecount-4.3.0/c» dh_auto_build --sourcedirectory=perl cd perl && make -j4 make[2]: ingresso nella directory «/build/allelecount-4.3.0/perl» cp lib/Sanger/CGP/AlleleCount.pm blib/lib/Sanger/CGP/AlleleCount.pm cp lib/Sanger/CGP/AlleleCount/Genotype.pm blib/lib/Sanger/CGP/AlleleCount/Genotype.pm cp lib/Sanger/CGP/AlleleCount/ToJson.pm blib/lib/Sanger/CGP/AlleleCount/ToJson.pm cp 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]: uscita dalla directory «/build/allelecount-4.3.0/perl» make[1]: uscita dalla directory «/build/allelecount-4.3.0» debian/rules override_dh_auto_test make[1]: ingresso nella directory «/build/allelecount-4.3.0» dh_auto_test --sourcedirectory=c cd c && make -j4 test make[2]: ingresso nella 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]: uscita dalla directory «/build/allelecount-4.3.0/c» dh_auto_test --sourcedirectory=perl cd perl && make -j4 test TEST_VERBOSE=1 make[2]: ingresso nella 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::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, 13 wallclock secs ( 0.26 usr 0.04 sys + 7.21 cusr 1.22 csys = 8.73 CPU) Result: PASS make[2]: uscita dalla directory «/build/allelecount-4.3.0/perl» make[1]: uscita dalla directory «/build/allelecount-4.3.0» create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: ingresso nella directory «/build/allelecount-4.3.0» dh_auto_install --sourcedirectory=c dh_auto_install --sourcedirectory=perl cd perl && make -j4 install DESTDIR=/build/allelecount-4.3.0/debian/tmp AM_UPDATE_INFO_DIR=no PREFIX=/usr make[2]: ingresso nella 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/alleleCounter.pl Installing /build/allelecount-4.3.0/debian/tmp/usr/bin/alleleCounterToJson.pl make[2]: uscita dalla directory «/build/allelecount-4.3.0/perl» make[1]: uscita dalla 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: generazione del pacchetto "allelecount-dbgsym" in "../allelecount-dbgsym_4.3.0-2_armhf.deb". dpkg-deb: generazione del pacchetto "allelecount" in "../allelecount_4.3.0-2_armhf.deb". dpkg-deb: generazione del pacchetto "liballelecount-perl" in "../liballelecount-perl_4.3.0-2_all.deb". dpkg-genbuildinfo --build=binary -O../allelecount_4.3.0-2_armhf.buildinfo dpkg-genchanges --build=binary -O../allelecount_4.3.0-2_armhf.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/9235/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/9235/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/9235 and its subdirectories I: Current time: Mon May 22 17:56:26 +14 2023 I: pbuilder-time-stamp: 1684727786