Fri May 10 02:13:52 UTC 2024 I: starting to build libseqlib/trixie/arm64 on jenkins on '2024-05-10 02:13' Fri May 10 02:13:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_8/10865/console.log Fri May 10 02:13:52 UTC 2024 I: Downloading source for trixie/libseqlib=1.2.0+dfsg-11 --2024-05-10 02:13:52-- http://deb.debian.org/debian/pool/main/libs/libseqlib/libseqlib_1.2.0%2bdfsg-11.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2401 (2.3K) [text/prs.lines.tag] Saving to: ‘libseqlib_1.2.0+dfsg-11.dsc’ 0K .. 100% 282M=0s 2024-05-10 02:13:52 (282 MB/s) - ‘libseqlib_1.2.0+dfsg-11.dsc’ saved [2401/2401] Fri May 10 02:13:52 UTC 2024 I: libseqlib_1.2.0+dfsg-11.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libseqlib Binary: libseqlib2, libseqlib-dev Architecture: any Version: 1.2.0+dfsg-11 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://github.com/walaj/SeqLib Standards-Version: 4.6.2 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 89ee20e44e0e76c6efce309a56e33556a76149bd 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Checksums-Sha256: 408ee92e5041ff45d9d259d1507ef783e74c565d02e0c623ef0a67a7c387b953 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 9e85fd66de1a1e1fcb576e045cfd1fefbeed75b222450032dfdc0b39a39ba2ea 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Files: 8d8f26bf4fd751789bbc53bd7319355a 148996 libseqlib_1.2.0+dfsg.orig.tar.xz 6f36289dd0bbde1824dc445037845166 15456 libseqlib_1.2.0+dfsg-11.debian.tar.xz Dgit: 279a189ccc52e73b124a50bcfe14717ee68c64d8 debian archive/debian/1.2.0+dfsg-11 https://git.dgit.debian.org/libseqlib -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmV7fQAUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdowIxAAxOwXiOsLHzl8ozOX9E3nR4m7iV6w /+2iDm3S90Xj/MRyr6A6BoJ7ikHHkIgICBHYAdsQJ1pAjkuMLd5QnKhGPyOieZjA JqwybgsoFhg5onEV1YXIFePTvyB5LbSEAFWa4J97do06AJjdnwpCEiszxvcdMQrC 3b4URe/BBdsB/eMcY/7R5Vs5L9xH1ol/vF9e0sxj8pOxX91rOkdXd0B4KQ70QJuq x4yCjF3O8cNl3ntE6+hizMBcVLqwMgo5BlmdfmS+sBGuLOBVxVkz0AZzhjfa1Uol jgesCiUP1UR8JeCmd+p4Y+Vxr2zRJlz6MAiJOxT8UfPh98PVyGnmeCTd8OL39OA5 AcT/JTlMDxXA1rv0sAMQkcJBlMPNHr+8zZWPbH2/GndaQgwnY8iQhILPbW4H5+YQ dOlKVNHZNOcWpZZwedR7yPybOfXIKl7CKQdlQFc6Kp6gsnRmXE6V9OR0JvhkuJRa 03o7/25eByPNYpHar7x1H3PXd/ksUOp78xP8RZad7MisAVzS+wz2dsQDSmwvgayK MxSCn18sCu/3USnrsRvMHg2BQHD2oIDx4ApxliCmIWdEsfq8ixEjFawTj/U2evV5 34zqyBvZPS9gaVq4N5Zush80tKxOq8NaY4SYejlvPSCUTSqVoPgOoIV+aml+zXAD cmcRNsM7KLyr36M= =JgTs -----END PGP SIGNATURE----- Fri May 10 02:13:52 UTC 2024 I: Checking whether the package is not for us Fri May 10 02:13:52 UTC 2024 I: Starting 1st build on remote node codethink02-arm64.debian.net. Fri May 10 02:13:52 UTC 2024 I: Preparing to do remote build '1' on codethink02-arm64.debian.net. Fri May 10 02:14:58 UTC 2024 I: Deleting $TMPDIR on codethink02-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu May 9 14:13:54 -12 2024 I: pbuilder-time-stamp: 1715307234 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 [libseqlib_1.2.0+dfsg-11.dsc] I: copying [./libseqlib_1.2.0+dfsg.orig.tar.xz] I: copying [./libseqlib_1.2.0+dfsg-11.debian.tar.xz] I: Extracting source gpgv: Signature made Thu Dec 14 22:09:04 2023 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-11.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-11.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/3739996/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' 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=12 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='ac5a77d56695433898c4c4aaecf91c92' 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='3739996' 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.HU23PkJ5/pbuilderrc_Ca00 --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/b1 --logfile b1/build.log libseqlib_1.2.0+dfsg-11.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink02-arm64 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 May 9 11:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3739996/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 ... 19744 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} libcom-err2{a} libcurl3t64-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libgssapi-krb5-2{a} libhts-dev{a} libhts3t64{a} libhtscodecs2{a} libicu72{a} libjsoncpp-dev{a} libjsoncpp25{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} libpipeline1{a} libpkgconf3{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libssw-dev{a} libssw0{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libyaml-0-2{a} m4{a} man-db{a} media-types{a} netbase{a} pkg-config{a} pkg-kde-tools{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-chardet{a} python3-debian{a} python3-minimal{a} python3-pkg-resources{a} python3-yaml{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libwww-perl lynx publicsuffix python3-apt wget zstd 0 packages upgraded, 85 newly installed, 0 to remove and 0 not upgraded. Need to get 31.6 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB] Get: 2 http://deb.debian.org/debian trixie/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB] Get: 3 http://deb.debian.org/debian trixie/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB] Get: 4 http://deb.debian.org/debian trixie/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB] Get: 5 http://deb.debian.org/debian trixie/main arm64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian trixie/main arm64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian trixie/main arm64 tzdata all 2024a-4 [255 kB] Get: 8 http://deb.debian.org/debian trixie/main arm64 readline-common all 8.2-4 [69.3 kB] Get: 9 http://deb.debian.org/debian trixie/main arm64 libreadline8t64 arm64 8.2-4 [157 kB] Get: 10 http://deb.debian.org/debian trixie/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB] Get: 11 http://deb.debian.org/debian trixie/main arm64 python3.11 arm64 3.11.9-1 [602 kB] Get: 12 http://deb.debian.org/debian trixie/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B] Get: 13 http://deb.debian.org/debian trixie/main arm64 python3 arm64 3.11.8-1 [27.4 kB] Get: 14 http://deb.debian.org/debian trixie/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 15 http://deb.debian.org/debian trixie/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 16 http://deb.debian.org/debian trixie/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 17 http://deb.debian.org/debian trixie/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 18 http://deb.debian.org/debian trixie/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 19 http://deb.debian.org/debian trixie/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 20 http://deb.debian.org/debian trixie/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 21 http://deb.debian.org/debian trixie/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 22 http://deb.debian.org/debian trixie/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 23 http://deb.debian.org/debian trixie/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 24 http://deb.debian.org/debian trixie/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 25 http://deb.debian.org/debian trixie/main arm64 autoconf all 2.71-3 [332 kB] Get: 26 http://deb.debian.org/debian trixie/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 27 http://deb.debian.org/debian trixie/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 28 http://deb.debian.org/debian trixie/main arm64 autopoint all 0.21-14 [496 kB] Get: 29 http://deb.debian.org/debian trixie/main arm64 d-shlibs all 0.106 [10.9 kB] Get: 30 http://deb.debian.org/debian trixie/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 31 http://deb.debian.org/debian trixie/main arm64 libtool all 2.4.7-7 [517 kB] Get: 32 http://deb.debian.org/debian trixie/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian trixie/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian trixie/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 35 http://deb.debian.org/debian trixie/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 36 http://deb.debian.org/debian trixie/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 37 http://deb.debian.org/debian trixie/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 38 http://deb.debian.org/debian trixie/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 39 http://deb.debian.org/debian trixie/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 40 http://deb.debian.org/debian trixie/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 41 http://deb.debian.org/debian trixie/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 42 http://deb.debian.org/debian trixie/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.15.3 [901 kB] Get: 45 http://deb.debian.org/debian trixie/main arm64 libbrotli1 arm64 1.1.0-2+b3 [295 kB] Get: 46 http://deb.debian.org/debian trixie/main arm64 libbwa-dev arm64 0.7.17-7+b3 [147 kB] Get: 47 http://deb.debian.org/debian trixie/main arm64 libbz2-dev arm64 1.0.8-5.1 [31.8 kB] Get: 48 http://deb.debian.org/debian trixie/main arm64 libcom-err2 arm64 1.47.1~rc2-1 [22.5 kB] Get: 49 http://deb.debian.org/debian trixie/main arm64 libkrb5support0 arm64 1.20.1-6+b1 [33.0 kB] Get: 50 http://deb.debian.org/debian trixie/main arm64 libk5crypto3 arm64 1.20.1-6+b1 [80.5 kB] Get: 51 http://deb.debian.org/debian trixie/main arm64 libkeyutils1 arm64 1.6.3-3 [9112 B] Get: 52 http://deb.debian.org/debian trixie/main arm64 libkrb5-3 arm64 1.20.1-6+b1 [315 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 libgssapi-krb5-2 arm64 1.20.1-6+b1 [124 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-6 [20.1 kB] Get: 55 http://deb.debian.org/debian trixie/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-6 [55.3 kB] Get: 56 http://deb.debian.org/debian trixie/main arm64 libldap-2.5-0 arm64 2.5.17+dfsg-1 [173 kB] Get: 57 http://deb.debian.org/debian trixie/main arm64 libnghttp2-14 arm64 1.61.0-1+b1 [71.0 kB] Get: 58 http://deb.debian.org/debian trixie/main arm64 libpsl5t64 arm64 0.21.2-1.1 [56.8 kB] Get: 59 http://deb.debian.org/debian trixie/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b4 [56.7 kB] Get: 60 http://deb.debian.org/debian trixie/main arm64 libssh2-1t64 arm64 1.11.0-4.1+b2 [207 kB] Get: 61 http://deb.debian.org/debian trixie/main arm64 libcurl3t64-gnutls arm64 8.7.1-3 [405 kB] Get: 62 http://deb.debian.org/debian trixie/main arm64 libcurl4-gnutls-dev arm64 8.7.1-3 [523 kB] Get: 63 http://deb.debian.org/debian trixie/main arm64 libdeflate0 arm64 1.20-1 [41.5 kB] Get: 64 http://deb.debian.org/debian trixie/main arm64 libdeflate-dev arm64 1.20-1 [50.5 kB] Get: 65 http://deb.debian.org/debian trixie/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 66 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg-3.1 [915 kB] Get: 67 http://deb.debian.org/debian trixie/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 68 http://deb.debian.org/debian trixie/main arm64 libhtscodecs2 arm64 1.6.0-1+b1 [71.6 kB] Get: 69 http://deb.debian.org/debian trixie/main arm64 libhts3t64 arm64 1.19+ds-1.1+b1 [413 kB] Get: 70 http://deb.debian.org/debian trixie/main arm64 liblzma-dev arm64 5.6.1+really5.4.5-1 [289 kB] Get: 71 http://deb.debian.org/debian trixie/main arm64 libhts-dev arm64 1.19+ds-1.1+b1 [1604 kB] Get: 72 http://deb.debian.org/debian trixie/main arm64 libjsoncpp25 arm64 1.9.5-6+b2 [73.2 kB] Get: 73 http://deb.debian.org/debian trixie/main arm64 libjsoncpp-dev arm64 1.9.5-6+b2 [24.8 kB] Get: 74 http://deb.debian.org/debian trixie/main arm64 libpkgconf3 arm64 1.8.1-1+b2 [35.3 kB] Get: 75 http://deb.debian.org/debian trixie/main arm64 libssw0 arm64 1.1-14+b1 [19.6 kB] Get: 76 http://deb.debian.org/debian trixie/main arm64 libssw-dev arm64 1.1-14+b1 [117 kB] Get: 77 http://deb.debian.org/debian trixie/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB] Get: 78 http://deb.debian.org/debian trixie/main arm64 pkgconf-bin arm64 1.8.1-1+b2 [29.3 kB] Get: 79 http://deb.debian.org/debian trixie/main arm64 pkgconf arm64 1.8.1-1+b2 [26.2 kB] Get: 80 http://deb.debian.org/debian trixie/main arm64 pkg-config arm64 1.8.1-1+b2 [14.0 kB] Get: 81 http://deb.debian.org/debian trixie/main arm64 python3-pkg-resources all 68.1.2-2 [241 kB] Get: 82 http://deb.debian.org/debian trixie/main arm64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 83 http://deb.debian.org/debian trixie/main arm64 python3-debian all 0.1.49 [115 kB] Get: 84 http://deb.debian.org/debian trixie/main arm64 python3-yaml arm64 6.0.1-2 [153 kB] Get: 85 http://deb.debian.org/debian trixie/main arm64 pkg-kde-tools all 0.17.1 [84.4 kB] Fetched 31.6 MB in 1s (58.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.2-4) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../6-libpython3.11-stdlib_3.11.9-1_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../7-python3.11_3.11.9-1_arm64.deb ... Unpacking python3.11 (3.11.9-1) ... 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Setting up libldap-2.5-0:arm64 (2.5.17+dfsg-1) ... Setting up pkgconf:arm64 (1.8.1-1+b2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-6+b1) ... Setting up pkg-config:arm64 (1.8.1-1+b2) ... Setting up libreadline8t64:arm64 (8.2-4) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.9-1) ... Setting up libcurl3t64-gnutls:arm64 (8.7.1-3) ... Setting up libcurl4-gnutls-dev:arm64 (8.7.1-3) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libhts3t64:arm64 (1.19+ds-1.1+b1) ... Setting up libpython3-stdlib:arm64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libhts-dev:arm64 (1.19+ds-1.1+b1) ... Setting up debhelper (13.15.3) ... Setting up python3 (3.11.8-1) ... Setting up python3-pkg-resources (68.1.2-2) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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-11_source.changes dpkg-buildpackage: info: source package libseqlib dpkg-buildpackage: info: source version 1.2.0+dfsg-11 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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(cached) yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking for zlib.h... yes checking for library containing gzopen... -lz checking for library containing lzma_code... -llzma checking for library containing BZ2_bzBuffToBuffDecompress... -lbz2 checking for library containing clock_gettime... none required checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for htslib... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/seqtools/Makefile config.status: creating libseqlib.pc config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands dh_auto_build make -j12 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make all-recursive make[2]: Entering directory 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'./'`FermiAssembler.cpp /bin/bash ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml `/usr/bin/pkg-config --cflags jsoncpp` -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c -o libseqlib_la-BamHeader.lo `test -f 'BamHeader.cpp' || echo './'`BamHeader.cpp libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c GenomicRegion.cpp -fPIC -DPIC -o .libs/libseqlib_la-GenomicRegion.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BWAWrapper.cpp -fPIC -DPIC -o .libs/libseqlib_la-BWAWrapper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c FermiAssembler.cpp -fPIC -DPIC -o .libs/libseqlib_la-FermiAssembler.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamHeader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamHeader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c RefGenome.cpp -fPIC -DPIC -o .libs/libseqlib_la-RefGenome.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamReader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c ReadFilter.cpp -fPIC -DPIC -o .libs/libseqlib_la-ReadFilter.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BFC.cpp -fPIC -DPIC -o .libs/libseqlib_la-BFC.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c FastqReader.cpp -fPIC -DPIC -o .libs/libseqlib_la-FastqReader.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamRecord.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamRecord.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamWriter.cpp -fPIC -DPIC -o .libs/libseqlib_la-BamWriter.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c SeqPlot.cpp -fPIC -DPIC -o .libs/libseqlib_la-SeqPlot.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c FastqReader.cpp -o libseqlib_la-FastqReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c RefGenome.cpp -o libseqlib_la-RefGenome.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BFC.cpp -o libseqlib_la-BFC.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamWriter.cpp -o libseqlib_la-BamWriter.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c FermiAssembler.cpp -o libseqlib_la-FermiAssembler.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamHeader.cpp -o libseqlib_la-BamHeader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BWAWrapper.cpp -o libseqlib_la-BWAWrapper.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamRecord.cpp -o libseqlib_la-BamRecord.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c SeqPlot.cpp -o libseqlib_la-SeqPlot.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c BamReader.cpp -o libseqlib_la-BamReader.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c ReadFilter.cpp -o libseqlib_la-ReadFilter.o >/dev/null 2>&1 libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I/usr/include -I/usr/include/htslib -I/usr/include/fml -I/usr/include/jsoncpp -Wno-sign-compare -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -c GenomicRegion.cpp -o libseqlib_la-GenomicRegion.o >/dev/null 2>&1 /bin/bash ../libtool --tag=CXX --mode=link g++ -g -std=c++11 -Wno-unknown-pragmas -g -O2 -ffile-prefix-map=/build/reproducible-path/libseqlib-1.2.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/13/../../../aarch64-linux-gnu/crti.o /usr/lib/gcc/aarch64-linux-gnu/13/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/13 -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu -L/usr/lib/gcc/aarch64-linux-gnu/13/../../../../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/13/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib/gcc/aarch64-linux-gnu/13/crtendS.o /usr/lib/gcc/aarch64-linux-gnu/13/../../../aarch64-linux-gnu/crtn.o -g -g -O2 -fstack-protector-strong -mbranch-protection=standard -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/reproducible-path/libseqlib-1.2.0+dfsg/src' make[3]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[3]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' dh_auto_test make -j12 check "TESTSUITEFLAGS=-j12 --verbose" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' Making check in src make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' make[2]: Nothing to be done for 'check'. make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg/src' make[2]: Entering directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[2]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' make[1]: Leaving directory '/build/reproducible-path/libseqlib-1.2.0+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install make -j1 install DESTDIR=/build/reproducible-path/libseqlib-1.2.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/libseqlib-1.2.0+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/libseqlib-1.2.0+dfsg/src/.libs/libseqlib.so.2 debian/libseqlib2/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/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/reproducible-path/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/aarch64-linux-gnu/pkgconfig mv libseqlib.pc /build/reproducible-path/libseqlib-1.2.0+dfsg/debian/libseqlib-dev/usr/lib/aarch64-linux-gnu/pkgconfig make[1]: Leaving directory '/build/reproducible-path/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 bwa_verbose 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_read used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries 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 bns_destroy 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_fclose used by debian/libseqlib2/usr/lib/aarch64-linux-gnu/libseqlib.so.2.0.0 found in none of the libraries dpkg-shlibdeps: warning: symbol nst_nt4_table 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 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 bwt_bwtupdate_core 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' in '../libseqlib2_1.2.0+dfsg-11_arm64.deb'. dpkg-deb: building package 'libseqlib2-dbgsym' in '../libseqlib2-dbgsym_1.2.0+dfsg-11_arm64.deb'. dpkg-deb: building package 'libseqlib-dev' in '../libseqlib-dev_1.2.0+dfsg-11_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libseqlib_1.2.0+dfsg-11_arm64.buildinfo dpkg-genchanges --build=binary -O../libseqlib_1.2.0+dfsg-11_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/3739996 and its subdirectories I: Current time: Thu May 9 14:14:57 -12 2024 I: pbuilder-time-stamp: 1715307297 Fri May 10 02:14:59 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Fri May 10 02:14:59 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Fri May 10 02:17:24 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Fri May 10 02:17:24 UTC 2024 I: libseqlib_1.2.0+dfsg-11_arm64.changes: Format: 1.8 Date: Thu, 14 Dec 2023 23:01:06 +0100 Source: libseqlib Binary: libseqlib-dev libseqlib2 libseqlib2-dbgsym Architecture: arm64 Version: 1.2.0+dfsg-11 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: 1047821 Changes: libseqlib (1.2.0+dfsg-11) unstable; urgency=medium . * d/clean: new: cleanup leftovers. (Closes: #1047821) Checksums-Sha1: d1ad6b4959c132e109dc6cf3fd8fa6b1fca94e55 207616 libseqlib-dev_1.2.0+dfsg-11_arm64.deb 3aecae7169183eceef3dc218709dc6e356ab875e 2151268 libseqlib2-dbgsym_1.2.0+dfsg-11_arm64.deb a913fcd6c941ccab1bc9d53f1221582e0fdd5243 144480 libseqlib2_1.2.0+dfsg-11_arm64.deb 6708ba7e68a79c2bcdac64dbd815bdcc3411debb 7645 libseqlib_1.2.0+dfsg-11_arm64.buildinfo Checksums-Sha256: b9c41ea27a15354fdfd333fe744768186a4ac3d88ef22672cdfae25cb1b2cea7 207616 libseqlib-dev_1.2.0+dfsg-11_arm64.deb f0e93d7b00e5000f3deb1134ef7cea860e03766048442467fef6786818f5b41a 2151268 libseqlib2-dbgsym_1.2.0+dfsg-11_arm64.deb 0181e077597ff66139b2012aa3c7a17446345efe8c548f2350df497a4664c479 144480 libseqlib2_1.2.0+dfsg-11_arm64.deb fa3001beea54a36f8251210644d50c77bf058a76d039327062e1ba74b4815df5 7645 libseqlib_1.2.0+dfsg-11_arm64.buildinfo Files: e801f871814ebd03eaa182f2f0503d22 207616 libdevel optional libseqlib-dev_1.2.0+dfsg-11_arm64.deb 91f215a5ce044d5c6e7dc517d06a1260 2151268 debug optional libseqlib2-dbgsym_1.2.0+dfsg-11_arm64.deb 62438698d2de9184d542cb432cfaf2ad 144480 libs optional libseqlib2_1.2.0+dfsg-11_arm64.deb c021056abbe335ba154ee3c33ae1cf89 7645 science optional libseqlib_1.2.0+dfsg-11_arm64.buildinfo Fri May 10 02:17:25 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_8-10865.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/libseqlib_1.2.0+dfsg-11.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/libseqlib_1.2.0+dfsg-11.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/libseqlib_1.2.0+dfsg-11.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/b1/libseqlib_1.2.0+dfsg-11_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.HU23PkJ5/b2/libseqlib_1.2.0+dfsg-11_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: 0.497s) 0.497s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.053s) 0.053s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 897ms CPU time consumed: 896ms Fri May 10 02:17:27 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Fri May 10 02:17:27 UTC 2024 I: libseqlib from trixie built successfully and reproducibly on arm64. Fri May 10 02:17:28 UTC 2024 I: Submitting .buildinfo files to external archives: Fri May 10 02:17:28 UTC 2024 I: Submitting 12K b1/libseqlib_1.2.0+dfsg-11_arm64.buildinfo.asc Fri May 10 02:17:29 UTC 2024 I: Submitting 12K b2/libseqlib_1.2.0+dfsg-11_arm64.buildinfo.asc Fri May 10 02:17:30 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri May 10 02:17:30 UTC 2024 I: Done submitting .buildinfo files. Fri May 10 02:17:30 UTC 2024 I: Removing signed libseqlib_1.2.0+dfsg-11_arm64.buildinfo.asc files: removed './b1/libseqlib_1.2.0+dfsg-11_arm64.buildinfo.asc' removed './b2/libseqlib_1.2.0+dfsg-11_arm64.buildinfo.asc'