Sun Apr 30 20:14:06 UTC 2023 I: starting to build libseqlib/bookworm/arm64 on jenkins on '2023-04-30 20:14' Sun Apr 30 20:14:06 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_14/7947/console.log Sun Apr 30 20:14:06 UTC 2023 I: Downloading source for bookworm/libseqlib=1.2.0+dfsg-9 --2023-04-30 20:14:06-- http://cdn-fastly.deb.debian.org/debian/pool/main/libs/libseqlib/libseqlib_1.2.0%2bdfsg-9.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2396 (2.3K) [text/prs.lines.tag] Saving to: ‘libseqlib_1.2.0+dfsg-9.dsc’ 0K .. 100% 47.6M=0s 2023-04-30 20:14:06 (47.6 MB/s) - ‘libseqlib_1.2.0+dfsg-9.dsc’ saved [2396/2396] Sun Apr 30 20:14:06 UTC 2023 I: libseqlib_1.2.0+dfsg-9.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libseqlib Binary: libseqlib2, libseqlib-dev Architecture: any Version: 1.2.0+dfsg-9 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/walaj/SeqLib Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/libseqlib Vcs-Git: https://salsa.debian.org/med-team/libseqlib.git Build-Depends: debhelper-compat (= 13), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev Package-List: libseqlib-dev deb libdevel optional arch=any libseqlib2 deb libs optional arch=any Checksums-Sha1: 584cb70cc2d11d595f26ec50763d11ca570395c5 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 89fbbbd8cf6d8daefa7e5b10d1d277da60e9e09f 15116 libseqlib_1.2.0+dfsg-9.debian.tar.xz Checksums-Sha256: 408ee92e5041ff45d9d259d1507ef783e74c565d02e0c623ef0a67a7c387b953 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 31ffae5e373c3977c90df89fc379590093bfa97bd842e2f75762539e4b1510f8 15116 libseqlib_1.2.0+dfsg-9.debian.tar.xz Files: 8d8f26bf4fd751789bbc53bd7319355a 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 75f6ebe1753a906baf2896173ce67e7a 15116 libseqlib_1.2.0+dfsg-9.debian.tar.xz Dgit: a7992faea79ba476bb9f4f25dc3ad5f2b6b1c0c6 debian archive/debian/1.2.0+dfsg-9 https://git.dgit.debian.org/libseqlib -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmLOW9wUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdrs0A//UeTq2pFG+aPYvuly6Fx8V8BkoKqm D3Dlogn3UeUjOkLTPQB9ik6qvRBFe0PhmHPLk1sz0Xutl9Sc9E0qzpPLHNev31F4 S9hO2O6amY1h/Bl6cjByQu8ucj5fV0S3CjFxLctl7n5JhCY7mQ71Q58n7ZrrIwWC UnPtp2ggOGDk2q4nExkpB3pqrmxKho3hUtw6cVm8VQb51QDeuQxNwjwPqAdj77xI FCHgha9BCOqyu/EkJmjr5j5mzXon73l//vzXPAO3E/ia+EvZv/ZmR3lyrisqIpKL Hml4hNBv0jOiT9aHf4puMv8m/EhGXaiOVRGjKlCU5tfVehfaqylRHxWmWsJ251ga 6xYTYc8YdWAT26O48ePeuXnNSDKUh69MGgA0/rLTxZ8PXogO0BgyFD48XqUxyOoK h11xyFrhHG8GLIPg3pLKjd5oEYwvQ6rK/Wru7iVcy2RC6TpvWCu2YkFQDu+zWqdx 6gLV/ztTAjLsXGRNuk8vHMx4PkMEaJKYo5WK8GkP7F4kE4Qnt1X37o1qaPOktBDY oPQfiGJkLP6NvwEcrE5MQrhVNXDgVlMV0tC+JMRTVOSg0vDvd+greDI7AbZvadXm AarG7aN4BDnedvyNUBhotkfOHSzxproTW7RCwtIQfMq6fm4EbdTvUYbhXej5h8CH omqkzW+IHo0bxoE= =jdJm -----END PGP SIGNATURE----- Sun Apr 30 20:14:06 UTC 2023 I: Checking whether the package is not for us Sun Apr 30 20:14:07 UTC 2023 I: Starting 1st build on remote node codethink12-arm64.debian.net. Sun Apr 30 20:14:07 UTC 2023 I: Preparing to do remote build '1' on codethink12-arm64.debian.net. Sun Apr 30 20:16:11 UTC 2023 I: Deleting $TMPDIR on codethink12-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 30 08:14:09 -12 2023 I: pbuilder-time-stamp: 1682885649 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 [libseqlib_1.2.0+dfsg-9.dsc] I: copying [./libseqlib_1.2.0+dfsg.orig.tar.xz] I: copying [./libseqlib_1.2.0+dfsg-9.debian.tar.xz] I: Extracting source gpgv: Signature made Tue Jul 12 17:45:00 2022 -12 gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA gpgv: issuer "emollier@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./libseqlib_1.2.0+dfsg-9.dsc: no acceptable signature found dpkg-source: info: extracting libseqlib in libseqlib-1.2.0+dfsg dpkg-source: info: unpacking libseqlib_1.2.0+dfsg.orig.tar.xz dpkg-source: info: unpacking libseqlib_1.2.0+dfsg-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs.patch dpkg-source: info: applying adapt_to_debian_fermi-lite.patch dpkg-source: info: applying fix_fermi-lite_usage.patch dpkg-source: info: applying fix_htslib_usage.patch dpkg-source: info: applying fml_include_path.patch dpkg-source: info: applying dynamic_lib.patch dpkg-source: info: applying use_debian_packaged_jsoncpp.patch dpkg-source: info: applying use_debian_packaged_ssw.patch dpkg-source: info: applying pkg-config.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/10590/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='10590' 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.rO0zi653/pbuilderrc_uy5Y --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.rO0zi653/b1 --logfile b1/build.log libseqlib_1.2.0+dfsg-9.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 4.15.0-210-generic #221-Ubuntu SMP Tue Apr 18 08:32:48 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 26 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/10590/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), d-shlibs, pkg-config, pkg-kde-tools, libhts-dev, libcurl4-gnutls-dev | libcurl4-dev, zlib1g-dev, libfml-dev (>= 0.1+git20190320.b499514), libbwa-dev, libjsoncpp-dev, libssw-dev, libbz2-dev 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 d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on pkg-kde-tools; however: Package pkg-kde-tools is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev; however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl4-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl4-dev is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev (>= 0.1+git20190320.b499514); however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on libbwa-dev; however: Package libbwa-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libssw-dev; however: Package libssw-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev 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} d-shlibs{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} libbwa-dev{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} pkg-kde-tools{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} readline-common{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 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libwww-perl lynx publicsuffix wget 0 packages upgraded, 72 newly installed, 0 to remove and 0 not upgraded. Need to get 29.4 MB of archives. After unpacking 116 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 d-shlibs all 0.104 [18.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 33 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libbwa-dev arm64 0.7.17-7+b2 [147 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-9 [357 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-9 [466 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 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 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp-dev arm64 1.9.5-4 [26.4 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libssw0 arm64 1.1-13 [18.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libssw-dev arm64 1.1-13 [21.9 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 pkg-kde-tools all 0.15.38 [97.8 kB] Fetched 29.4 MB in 1s (26.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. 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Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 19932 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.deb ... 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Setting up libhtscodecs2:arm64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libpsl5:arm64 (0.21.2-1) ... Setting up libicu72:arm64 (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 libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (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 libfml0:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libpkgconf3:arm64 (1.8.1-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (1.9.5-4) ... 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Setting up libhts-dev:arm64 (1.16+ds-3) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up pkg-kde-tools (0.15.38) ... 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 I: Building the package I: Running cd /build/libseqlib-1.2.0+dfsg/ && 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 > ../libseqlib_1.2.0+dfsg-9_source.changes dpkg-buildpackage: info: source package libseqlib dpkg-buildpackage: info: source version 1.2.0+dfsg-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --with pkgkde_symbolshelper dh_clean debian/rules binary dh binary --with pkgkde_symbolshelper dh_update_autotools_config dh_autoreconf libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.ac, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. libtoolize: 'AC_PROG_RANLIB' is rendered obsolete by 'LT_INIT' configure.ac:6: warning: The macro `AC_CONFIG_HEADER' is obsolete. configure.ac:6: You should run autoupdate. ./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from... configure.ac:6: the top level configure.ac:19: warning: The macro `AC_PROG_LIBTOOL' is obsolete. configure.ac:19: You should run autoupdate. aclocal.m4:122: AC_PROG_LIBTOOL is expanded from... configure.ac:19: the top level configure.ac:17: installing './compile' configure.ac:19: installing './config.guess' configure.ac:19: installing './config.sub' configure.ac:4: installing './install-sh' configure.ac:4: installing './missing' src/Makefile.am: installing './depcomp' dh_auto_configure ./configure --build=aarch64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/aarch64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for g++... g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether g++ accepts -g... yes checking for g++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of g++... none checking for gcc... gcc checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking dependency style of gcc... none checking for ranlib... ranlib checking build system type... aarch64-unknown-linux-gnu checking host system type... aarch64-unknown-linux-gnu checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 1572864 checking how to convert aarch64-unknown-linux-gnu file names to aarch64-unknown-linux-gnu format... func_convert_file_noop checking how to convert aarch64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... 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-std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -version-info 2:0 -lfml `/usr/bin/pkg-config --libs htslib` `/usr/bin/pkg-config --libs jsoncpp` -lssw -Wl,-z,relro -Wl,-z,now -o libseqlib.la -rpath /usr/lib/aarch64-linux-gnu libseqlib_la-FastqReader.lo libseqlib_la-BFC.lo libseqlib_la-ReadFilter.lo libseqlib_la-SeqPlot.lo libseqlib_la-GenomicRegion.lo libseqlib_la-RefGenome.lo libseqlib_la-BamWriter.lo libseqlib_la-BamReader.lo libseqlib_la-BWAWrapper.lo libseqlib_la-BamRecord.lo libseqlib_la-FermiAssembler.lo libseqlib_la-BamHeader.lo -lbz2 -llzma -lz -pthread libtool: link: g++ -fPIC -DPIC -shared -nostdlib /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/12/crtbeginS.o .libs/libseqlib_la-FastqReader.o .libs/libseqlib_la-BFC.o .libs/libseqlib_la-ReadFilter.o .libs/libseqlib_la-SeqPlot.o .libs/libseqlib_la-GenomicRegion.o .libs/libseqlib_la-RefGenome.o .libs/libseqlib_la-BamWriter.o .libs/libseqlib_la-BamReader.o .libs/libseqlib_la-BWAWrapper.o .libs/libseqlib_la-BamRecord.o .libs/libseqlib_la-FermiAssembler.o .libs/libseqlib_la-BamHeader.o -lfml -lhts -ljsoncpp -lssw -lbz2 -llzma -lz -L/usr/lib/gcc/aarch64-linux-gnu/12 -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/12/../../../../lib -L/lib/aarch64-linux-gnu -L/lib/../lib -L/usr/lib/aarch64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/aarch64-linux-gnu/12/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/12/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/12/../../../aarch64-linux-gnu/crtn.o -g -g -O2 -fstack-protector-strong -Wl,-z -Wl,relro -Wl,-z -Wl,now -pthread -Wl,-soname -Wl,libseqlib.so.2 -o .libs/libseqlib.so.2.0.0 libtool: link: (cd ".libs" && rm -f "libseqlib.so.2" && ln -s "libseqlib.so.2.0.0" "libseqlib.so.2") libtool: link: (cd ".libs" && rm -f "libseqlib.so" && ln -s "libseqlib.so.2.0.0" "libseqlib.so") libtool: link: ar cr .libs/libseqlib.a libseqlib_la-FastqReader.o libseqlib_la-BFC.o libseqlib_la-ReadFilter.o libseqlib_la-SeqPlot.o libseqlib_la-GenomicRegion.o libseqlib_la-RefGenome.o libseqlib_la-BamWriter.o libseqlib_la-BamReader.o libseqlib_la-BWAWrapper.o libseqlib_la-BamRecord.o libseqlib_la-FermiAssembler.o libseqlib_la-BamHeader.o libtool: link: ranlib .libs/libseqlib.a libtool: link: ( cd ".libs" && rm -f "libseqlib.la" && ln -s "../libseqlib.la" "libseqlib.la" ) make[3]: Leaving directory '/build/libseqlib-1.2.0+dfsg/src' make[3]: Entering directory '/build/libseqlib-1.2.0+dfsg' make[3]: Leaving directory '/build/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/libseqlib-1.2.0+dfsg' dh_auto_test make -j8 check "TESTSUITEFLAGS=-j8 --verbose" VERBOSE=1 make[1]: Entering directory '/build/libseqlib-1.2.0+dfsg' Making check in src make[2]: Entering directory '/build/libseqlib-1.2.0+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/libseqlib-1.2.0+dfsg/src' make[2]: Entering directory '/build/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/libseqlib-1.2.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/libseqlib-1.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/libseqlib-1.2.0+dfsg' echo "mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib" mkdir -p lib && cp src/libseqlib.a fermi-lite/libfml.a bwa/libbwa.a htslib/libhts.a lib make[1]: Leaving directory '/build/libseqlib-1.2.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/libseqlib-1.2.0+dfsg' dh_install # Trick to get also headers moved by d-shlibmove cp -a SeqLib debian # note: also GenomicRegionCollection.cpp is really needed by freebayes d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/SeqLib usr/include \ --override s/libfml0-dev/libfml-dev/ \ --override s/libssw0-dev/libssw-dev/ \ src/.libs/libseqlib.so Library package automatic movement utility --> libfml-dev package exists. --> libhts-dev package exists. --> libjsoncpp-dev package exists. --> libssw-dev package exists. --> zlib1g-dev package exists. set -e install -d -m 755 debian/libseqlib-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libseqlib2/usr/lib/aarch64-linux-gnu mv src/.libs/libseqlib.a debian/libseqlib-dev/usr/lib/aarch64-linux-gnu mv src/.libs/libseqlib.so debian/libseqlib-dev/usr/lib/aarch64-linux-gnu mv /build/libseqlib-1.2.0+dfsg/src/.libs/libseqlib.so.2 debian/libseqlib2/usr/lib/aarch64-linux-gnu mv /build/libseqlib-1.2.0+dfsg/src/.libs/libseqlib.so.2.0.0 debian/libseqlib2/usr/lib/aarch64-linux-gnu PKGDEV=libseqlib-dev PKGSHL=libseqlib2 install -d -m 755 debian/libseqlib-dev/usr/include mv debian/SeqLib debian/libseqlib-dev/usr/include mkdir -p /build/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv libseqlib.pc /build/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/aarch64-linux-gnu/pkgconfig make[1]: Leaving directory '/build/libseqlib-1.2.0+dfsg' dh_installdocs dh_installchangelogs 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 dpkg-shlibdeps: warning: symbol bwt_cal_sa used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol kseq_init used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bns_dump used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_fflush used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwa_fill_scmat used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol bwa_idx_load used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol is_bwt used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_xopen_core used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol mem_align1 used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol err_fclose used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: 11 other similar warnings have been skipped (use -v to see them all) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libseqlib2-dbgsym' in '../libseqlib2-dbgsym_1.2.0+dfsg-9_arm64.deb'. dpkg-deb: building package 'libseqlib2' in '../libseqlib2_1.2.0+dfsg-9_arm64.deb'. dpkg-deb: building package 'libseqlib-dev' in '../libseqlib-dev_1.2.0+dfsg-9_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libseqlib_1.2.0+dfsg-9_arm64.buildinfo dpkg-genchanges --build=binary -O../libseqlib_1.2.0+dfsg-9_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/10590 and its subdirectories I: Current time: Sun Apr 30 08:16:09 -12 2023 I: pbuilder-time-stamp: 1682885769 Sun Apr 30 20:16:11 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink11-arm64.debian.net. Sun Apr 30 20:16:11 UTC 2023 I: Preparing to do remote build '2' on codethink11-arm64.debian.net. Sun Apr 30 20:21:25 UTC 2023 I: Deleting $TMPDIR on codethink11-arm64.debian.net. Sun Apr 30 20:21:25 UTC 2023 I: libseqlib_1.2.0+dfsg-9_arm64.changes: Format: 1.8 Date: Wed, 13 Jul 2022 07:34:09 +0200 Source: libseqlib Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym Architecture: arm64 Version: 1.2.0+dfsg-9 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libseqlib-dev - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat libseqlib2 - C++ htslib/bwa-mem/fermi interface for interrogating sequence dat Closes: 1012992 Changes: libseqlib (1.2.0+dfsg-9) unstable; urgency=medium . * d/control: add myself to uploaders. * d/libseqlib2.symbols.amd64: refresh list of optional symbols. Closes: #1012992 * Standards-Version: 4.6.1 (routine-update) Checksums-Sha1: eab217fba3d3f9b1c6eaa11d549d2cfd9948899b 202048 libseqlib-dev_1.2.0+dfsg-9_arm64.deb 1f53f936cf08fdc7e949e89aefd10aa1d7c42431 2229504 libseqlib2-dbgsym_1.2.0+dfsg-9_arm64.deb 617b9aac4d18ba73e4d40d1131614d16feeb1252 140580 libseqlib2_1.2.0+dfsg-9_arm64.deb 4d8243a9f5a12b06bfa163f9ee207942b754af12 7216 libseqlib_1.2.0+dfsg-9_arm64.buildinfo Checksums-Sha256: c9cf783d17fc3de92d9526ee947f7318ab7efab8dcca751ebb507031587c0e62 202048 libseqlib-dev_1.2.0+dfsg-9_arm64.deb 01b1d658cfe620fcefa26dfb79a635694f996667e48e89d0ee6049ea7f2b6777 2229504 libseqlib2-dbgsym_1.2.0+dfsg-9_arm64.deb be1d7c6726991a9686031bfaeb23d3299710efae7c2463289e125d548dcb7852 140580 libseqlib2_1.2.0+dfsg-9_arm64.deb 3e92d41f5401eeb60193610be78b20ba8ae3058f0549923cb12a17f32d604f76 7216 libseqlib_1.2.0+dfsg-9_arm64.buildinfo Files: fcbfd23906c5caed583d58a853b32ddd 202048 libdevel optional libseqlib-dev_1.2.0+dfsg-9_arm64.deb da90fd0587dacae8978d7d0e2d627355 2229504 debug optional libseqlib2-dbgsym_1.2.0+dfsg-9_arm64.deb d7052006c2df5ad6da6fd2a4828d34bd 140580 libs optional libseqlib2_1.2.0+dfsg-9_arm64.deb cea0f0ce6b684cd54dcabd4fa2b5bf3d 7216 science optional libseqlib_1.2.0+dfsg-9_arm64.buildinfo Sun Apr 30 20:21:27 UTC 2023 I: diffoscope 241 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.rO0zi653/libseqlib_1.2.0+dfsg-9.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.rO0zi653/libseqlib_1.2.0+dfsg-9.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.rO0zi653/libseqlib_1.2.0+dfsg-9.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.rO0zi653/b1/libseqlib_1.2.0+dfsg-9_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.rO0zi653/b2/libseqlib_1.2.0+dfsg-9_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 1.490s) 1.490s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.120s) 0.120s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Sun Apr 30 20:21:30 UTC 2023 I: diffoscope 241 found no differences in the changes files, and a .buildinfo file also exists. Sun Apr 30 20:21:30 UTC 2023 I: libseqlib from bookworm built successfully and reproducibly on arm64. Sun Apr 30 20:21:32 UTC 2023 I: Submitting .buildinfo files to external archives: Sun Apr 30 20:21:32 UTC 2023 I: Submitting 8.0K b1/libseqlib_1.2.0+dfsg-9_arm64.buildinfo.asc Sun Apr 30 20:21:34 UTC 2023 I: Submitting 8.0K b2/libseqlib_1.2.0+dfsg-9_arm64.buildinfo.asc Sun Apr 30 20:21:35 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sun Apr 30 20:21:35 UTC 2023 I: Done submitting .buildinfo files. Sun Apr 30 20:21:35 UTC 2023 I: Removing signed libseqlib_1.2.0+dfsg-9_arm64.buildinfo.asc files: removed './b1/libseqlib_1.2.0+dfsg-9_arm64.buildinfo.asc' removed './b2/libseqlib_1.2.0+dfsg-9_arm64.buildinfo.asc'