Thu Apr 20 11:53:28 UTC 2023 I: starting to build pbdagcon/bookworm/arm64 on jenkins on '2023-04-20 11:53' Thu Apr 20 11:53:28 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_24/11249/console.log Thu Apr 20 11:53:28 UTC 2023 I: Downloading source for bookworm/pbdagcon=0.3+git20180411.c14c422+dfsg-8 --2023-04-20 11:53:28-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/pbdagcon/pbdagcon_0.3%2bgit20180411.c14c422%2bdfsg-8.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2397 (2.3K) [text/prs.lines.tag] Saving to: ‘pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc’ 0K .. 100% 1.88M=0.001s 2023-04-20 11:53:28 (1.88 MB/s) - ‘pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc’ saved [2397/2397] Thu Apr 20 11:53:28 UTC 2023 I: pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: pbdagcon Binary: pbdagcon Architecture: any Version: 0.3+git20180411.c14c422+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/PacificBiosciences/pbdagcon Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/pbdagcon Vcs-Git: https://salsa.debian.org/med-team/pbdagcon.git Testsuite: autopkgtest Testsuite-Triggers: blasr, daligner, dazzdb Build-Depends: debhelper-compat (= 13), python3:any, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev (>= 5.3.5+dfsg-4~), libpbbam-dev, libpbdata-dev (>= 5.3.5+dfsg-4~), libpbcopper-dev, libpbihdf-dev (>= 5.3.5+dfsg-4~), googletest Package-List: pbdagcon deb science optional arch=any Checksums-Sha1: 12afc3055828fc218ccab4e287d9e665ce6dec3a 79760 pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz fb6b6645e3cd29858f56d1e989c3bfb17de8fd6a 58060 pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz Checksums-Sha256: f554fedfaa673cb22bebb28d941139e72a1a9284039929c92b16d9c58fc1f8b9 79760 pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz 3b052db243a603e23180ce95b67f0fc23d72c46969d8bc9f0e66346413f1642a 58060 pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz Files: 675f3ae464f2315b689464c5ce3dd1e7 79760 pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz 4bb2d2c96854e9db643ef4fbf4d3f228 58060 pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmIpjeMSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nx/v8P/jK5MttzDzC2GYgLcIXCFcNSW+mGMu8F YGqbMfNy9OF98eR4qI2SJwAS31kTZPQl24zg6q398GNRES2WsNmQ+Ph2Z0oqmWQV 4XeDOPaz0nczvQy1xG3iLZgg2LH7UUsHJecqCrWZLCLaTq20FBsEyjvfWvVV+Evy FJg2XZwfFbgGYnBph2Jvvd6h3nPgMRVQk+d17QE9aqBj991nHShQeaGeJrrH6LSd 3QuXeL35gd6SRF8xyiJPKsLoCh0Eslcx/SpIEWRWIEiMumki6VO9wVQ+hohl/i7v NVsXAmEgGCVlwoVchs2coUB1MPwtHamL+jE28yZkQTvTWyiRZSlaylzvw/YW1hsR RcJqT4uvDhkOkdMFw3uC+BoROHfi3/s7yCY+Re4ftO+EAOK0A8G11mr50txmRvhx uz6UgKskxsrzhsN0k1XrMtBoH3IP3zeJRjBr0qUrAx8D+SpAQrrr8BgXpcOG/FYs 4vMGxjqPffVa562dx5YJ8MXaNZv0l6/VXKkMkTKGFhtL/mwzeh8McQTb5YOhSjb/ 2PWJTT/Jnb8g0zAsQDuxI5DBZk1BPQk25oDNgg7lDMvxu/Kl54JsD5cEj5fNehOQ 0XWZmRRjQmPouNWy3Jke6AyW0bVfzj+/8QWALW7LOZ6kh5IuUsdb4rLJ3v9bFC7s DevbCLHBSWcE =Uro/ -----END PGP SIGNATURE----- Thu Apr 20 11:53:28 UTC 2023 I: Checking whether the package is not for us Thu Apr 20 11:53:28 UTC 2023 I: Starting 1st build on remote node codethink14-arm64.debian.net. Thu Apr 20 11:53:28 UTC 2023 I: Preparing to do remote build '1' on codethink14-arm64.debian.net. Thu Apr 20 11:59:33 UTC 2023 I: Deleting $TMPDIR on codethink14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 19 23:53:31 -12 2023 I: pbuilder-time-stamp: 1681991611 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 [pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc] I: copying [./pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz] I: copying [./pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Mar 9 17:34:27 2022 -12 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "nilesh@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./pbdagcon_0.3+git20180411.c14c422+dfsg-8.dsc: no acceptable signature found dpkg-source: info: extracting pbdagcon in pbdagcon-0.3+git20180411.c14c422+dfsg dpkg-source: info: unpacking pbdagcon_0.3+git20180411.c14c422+dfsg.orig.tar.xz dpkg-source: info: unpacking pbdagcon_0.3+git20180411.c14c422+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying compiler-flags.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying libdata_libpbihdf.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17771/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='17771' 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.AGdGy8JL/pbuilderrc_QGK3 --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.AGdGy8JL/b1 --logfile b1/build.log pbdagcon_0.3+git20180411.c14c422+dfsg-8.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 codethink14-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 18 22:25 /bin -> usr/bin I: user script /srv/workspace/pbuilder/17771/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), python3:any, zlib1g-dev, libhdf5-dev, libboost-dev, libtclap-dev, libpbseq-dev (>= 5.3.5+dfsg-4~), libpbbam-dev, libpbdata-dev (>= 5.3.5+dfsg-4~), libpbcopper-dev, libpbihdf-dev (>= 5.3.5+dfsg-4~), googletest 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 python3:any. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-dev; however: Package libhdf5-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-dev; however: Package libboost-dev is not installed. pbuilder-satisfydepends-dummy depends on libtclap-dev; however: Package libtclap-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbseq-dev (>= 5.3.5+dfsg-4~); however: Package libpbseq-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbbam-dev; however: Package libpbbam-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbdata-dev (>= 5.3.5+dfsg-4~); however: Package libpbdata-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbcopper-dev; however: Package libpbcopper-dev is not installed. pbuilder-satisfydepends-dummy depends on libpbihdf-dev (>= 5.3.5+dfsg-4~); however: Package libpbihdf-dev is not installed. pbuilder-satisfydepends-dummy depends on googletest; however: Package googletest 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} googletest{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libblasr-dev{a} libblasr5.3.5{a} libboost-dev{a} libboost1.74-dev{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libldap-2.5-0{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpbbam-dev{a} libpbbam2.1.0{a} libpbcopper-dev{a} libpbcopper2.0.0{a} libpbdata-dev{a} libpbihdf-dev{a} libpbseq-dev{a} libpipeline1{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} libssl-dev{a} libsub-override-perl{a} libsz2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{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: ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 88 newly installed, 0 to remove and 0 not upgraded. Need to get 55.0 MB of archives. After unpacking 344 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 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 googletest all 1.12.1-0.2 [506 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 hdf5-helpers arm64 1.10.8+repack1-1 [27.9 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libaec0 arm64 1.0.6-1+b1 [19.9 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libsz2 arm64 1.0.6-1+b1 [7740 B] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libaec-dev arm64 1.0.6-1+b1 [18.7 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-8 [361 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libhdf5-103-1 arm64 1.10.8+repack1-1 [1037 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libhdf5-cpp-103-1 arm64 1.10.8+repack1-1 [119 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-8 [357 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 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 libpbcopper2.0.0 arm64 2.0.0+dfsg-2 [510 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libpbbam2.1.0 arm64 2.1.0+dfsg-2 [665 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libblasr5.3.5 arm64 5.3.5+dfsg-4+b2 [1040 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libpbcopper-dev arm64 2.0.0+dfsg-2 [846 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libpbdata-dev arm64 5.3.5+dfsg-4+b2 [41.5 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 libblasr-dev arm64 5.3.5+dfsg-4+b2 [2041 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-20 [9510 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-8 [466 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 libhdf5-fortran-102 arm64 1.10.8+repack1-1 [91.1 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-100 arm64 1.10.8+repack1-1 [64.0 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-fortran-100 arm64 1.10.8+repack1-1 [42.7 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libhdf5-hl-cpp-100 arm64 1.10.8+repack1-1 [25.4 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2 [292 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 libjpeg-dev arm64 1:2.1.5-2 [71.8 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.8-1 [2296 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 libhdf5-dev arm64 1.10.8+repack1-1 [2654 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 libpbbam-dev arm64 2.1.0+dfsg-2 [88.8 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 libpbihdf-dev arm64 5.3.5+dfsg-4+b2 [48.0 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libpbseq-dev arm64 5.3.5+dfsg-4+b2 [5776 B] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB] Fetched 55.0 MB in 5s (11.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19616 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. 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Unpacking libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 20366 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.17+nmu1_all.deb ... 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Selecting previously unselected package libtclap-dev. Preparing to unpack .../77-libtclap-dev_1.2.5-1+b1_arm64.deb ... Unpacking libtclap-dev (1.2.5-1+b1) ... 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 libboost1.74-dev:arm64 (1.74.0+ds1-20) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libpbcopper2.0.0:arm64 (2.0.0+dfsg-2) ... 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 googletest (1.12.1-0.2) ... Setting up libaec0:arm64 (1.0.6-1+b1) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libssl-dev:arm64 (3.0.8-1) ... Setting up autopoint (0.21-12) ... Setting up libpbcopper-dev:arm64 (2.0.0+dfsg-2) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up autoconf (2.71-3) ... Setting up libtclap-dev (1.2.5-1+b1) ... Setting up liblzma-dev:arm64 (5.4.1-0.2) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (1.10.0-3+b1) ... Setting up libboost-dev:arm64 (1.74.0.3) ... Setting up libdeflate-dev:arm64 (1.14-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Setting up libsz2:arm64 (1.0.6-1+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 libreadline8:arm64 (8.2-1.3) ... Setting up libaec-dev:arm64 (1.0.6-1+b1) ... Setting up libjpeg-dev:arm64 (1:2.1.5-2) ... Setting up libpbdata-dev:arm64 (5.3.5+dfsg-4+b2) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... 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 libcurl4:arm64 (7.88.1-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libcurl3-gnutls:arm64 (7.88.1-8) ... Setting up libcurl4-gnutls-dev:arm64 (7.88.1-8) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libhdf5-103-1:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-cpp-103-1:arm64 (1.10.8+repack1-1) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up libhdf5-hl-100:arm64 (1.10.8+repack1-1) ... Setting up python3.11 (3.11.2-6) ... Setting up libhts3:arm64 (1.16+ds-3) ... 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 libhdf5-hl-cpp-100:arm64 (1.10.8+repack1-1) ... Setting up libhdf5-fortran-102:arm64 (1.10.8+repack1-1) ... Setting up libpbbam2.1.0:arm64 (2.1.0+dfsg-2) ... Setting up libhdf5-hl-fortran-100:arm64 (1.10.8+repack1-1) ... Setting up libpbbam-dev:arm64 (2.1.0+dfsg-2) ... Setting up libblasr5.3.5:arm64 (5.3.5+dfsg-4+b2) ... Setting up libblasr-dev:arm64 (5.3.5+dfsg-4+b2) ... Setting up libhdf5-dev (1.10.8+repack1-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/aarch64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libpbihdf-dev (5.3.5+dfsg-4+b2) ... Setting up libpbseq-dev:arm64 (5.3.5+dfsg-4+b2) ... 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/pbdagcon-0.3+git20180411.c14c422+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 > ../pbdagcon_0.3+git20180411.c14c422+dfsg-8_source.changes dpkg-buildpackage: info: source package pbdagcon dpkg-buildpackage: info: source version 0.3+git20180411.c14c422+dfsg-8 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Nilesh Patra dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j8 clean make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp clean make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' rm -f *.d rm -f *.o rm -f pbdagcon rm -f dazcon make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make -C test/cpp clean make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp' rm -f .//*.o rm -f *.o rm -f test_* make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp' make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' ./configure.py --shared uname -s uname='Linux' writing to '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/defines.mk' """ DALIGNER_INCLUDE ?= ${DALIGNER_SRC} DALIGNER_SRC ?= /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include DAZZ_DB_INCLUDE ?= ${DAZZ_DB_SRC} DAZZ_DB_SRC ?= /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include GTEST_INCLUDE ?= /usr/src/googletest/googletest/include GTEST_SRC ?= /usr/src/googletest/googletest/src HDF5_LIB ?= /usr/lib/aarch64-linux-gnu/hdf5/serial HDF5_LIBFLAGS ?= -lhdf5_cpp -lhdf5 HTSLIB_LIBS ?= -lhts LIBBLASR_INCLUDE ?= /usr/include/pbseq/alignment LIBBLASR_LIBFLAGS ?= -lblasr LIBPBDATA_INCLUDE ?= /usr/include/pbseq/pbdata LIBPBIHDF_INCLUDE ?= /usr/include/pbseq/hdf PBBAM_INCLUDE ?= /usr/include/pbseq PBBAM_LIBFLAGS ?= -lpbbam PTHREAD_LIBFLAGS ?= -lpthread ZLIB_LIBFLAGS ?= -lz LDLIBS+=-lrt """ make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o Alignment.o Alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o AlnGraphBoost.o AlnGraphBoost.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o BlasrM5AlnProvider.o BlasrM5AlnProvider.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o main.o main.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o SimpleAligner.o SimpleAligner.cpp cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DB.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o QV.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/QV.c cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wextra -fno-strict-aliasing -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o align.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include/align.c /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c: In function 'Open_QVs': /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2415:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2415 | (void) fscanf(istub,DB_NFILE,&nfiles); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2419:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2419 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2424:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2424 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o DazAlnProvider.o DazAlnProvider.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wuninitialized -pedantic -Wdate-time -D_FORTIFY_SOURCE=2 -MMD -MP -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -isystem.//third-party -c -o dazcon.o dazcon.cpp g++ -o dazcon Alignment.o AlnGraphBoost.o DB.o QV.o align.o DazAlnProvider.o dazcon.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o pbdagcon Alignment.o AlnGraphBoost.o BlasrM5AlnProvider.o main.o SimpleAligner.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' dh_auto_test make -j8 check make[1]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' make -C src/cpp make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/src/cpp' make -C test/cpp make[2]: Entering directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp' g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest-all.o /usr/src/googletest/googletest/src/gtest-all.cc g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g -Wall -Wextra -pthread -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -isystem /usr/src/googletest/googletest/include -isystem /usr/src/googletest/googletest/src/.. -c -o gtest_main.o /usr/src/googletest/googletest/src/gtest_main.cc g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoost.o .//../../src/cpp/AlnGraphBoost.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o Alignment.o .//../../src/cpp/Alignment.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAligner.o .//../../src/cpp/SimpleAligner.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlnGraphBoostTest.o AlnGraphBoostTest.cpp mkdir xml g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o AlignmentTest.o AlignmentTest.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o SimpleAlignerTest.o SimpleAlignerTest.cpp cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o DB.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o QV.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/QV.c /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c: In function 'Open_QVs': /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2415:16: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2415 | (void) fscanf(istub,DB_NFILE,&nfiles); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2419:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2419 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include/DB.c:2424:20: warning: ignoring return value of 'fscanf' declared with attribute 'warn_unused_result' [-Wunused-result] 2424 | { (void) fscanf(istub,DB_FDATA,&last,fname,prolog); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o align.o /build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include/align.c g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o DazAlnProvider.o .//../../src/cpp/DazAlnProvider.cpp g++ -g -O2 -ffile-prefix-map=/build/pbdagcon-0.3+git20180411.c14c422+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -I. -I./ -I.//../../src/cpp -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/dazzdb-include -I/build/pbdagcon-0.3+git20180411.c14c422+dfsg/debian/daligner-include -I/usr/include/pbseq/alignment -I/usr/include/pbseq/pbdata -I/usr/include/pbseq/hdf -I/usr/include/pbseq -I/usr/src/googletest/googletest/include -Ithird-party -c -o TargetHitTest.o TargetHitTest.cpp g++ -o test-alngraph gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlnGraphBoostTest.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o test-alignment gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o AlignmentTest.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o test-simple_aligner gtest-all.o gtest_main.o AlnGraphBoost.o Alignment.o SimpleAligner.o SimpleAlignerTest.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread g++ -o test-target_hit gtest-all.o gtest_main.o DB.o QV.o align.o Alignment.o DazAlnProvider.o TargetHitTest.o -Wl,-z,relro -L /usr/lib/aarch64-linux-gnu/hdf5/serial -lrt -lblasr -lpbbam -lhdf5_cpp -lhdf5 -lhts -lz -lpthread LD_LIBRARY_PATH=::::/usr/lib/aarch64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-target_hit --gtest_output=xml:xml/test-target_hit.xml Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 3 tests from 1 test suite. [----------] Global test environment set-up. [----------] 3 tests from TargetHitTest [ RUN ] TargetHitTest.single_overlap_perfect [ OK ] TargetHitTest.single_overlap_perfect (0 ms) [ RUN ] TargetHitTest.single_overlap_inaccurate [ OK ] TargetHitTest.single_overlap_inaccurate (0 ms) [ RUN ] TargetHitTest.multi_overlap_inaccurate [ OK ] TargetHitTest.multi_overlap_inaccurate (0 ms) [----------] 3 tests from TargetHitTest (0 ms total) [----------] Global test environment tear-down [==========] 3 tests from 1 test suite ran. (0 ms total) [ PASSED ] 3 tests. LD_LIBRARY_PATH=::::/usr/lib/aarch64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alignment --gtest_output=xml:xml/test-alignment.xml LD_LIBRARY_PATH=::::/usr/lib/aarch64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-simple_aligner --gtest_output=xml:xml/test-simple_aligner.xml Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 4 tests from 1 test suite. [----------] Global test environment set-up. [----------] 4 tests from Alignment [ RUN ] Alignment.Normalize [ OK ] Alignment.Normalize (0 ms) [ RUN ] Alignment.ParseBasic [ OK ] Alignment.ParseBasic (0 ms) [ RUN ] Alignment.ParseQuery [ OK ] Alignment.ParseQuery (0 ms) [ RUN ] Alignment.Trim [ OK ] Alignment.Trim (0 ms) [----------] 4 tests from Alignment (0 ms total) [----------] Global test environment tear-down [==========] 4 tests from 1 test suite ran. (0 ms total) [ PASSED ] 4 tests. Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 1 test from 1 test suite. [----------] Global test environment set-up. [----------] 1 test from SimpleAligner [ RUN ] SimpleAligner.align [ OK ] SimpleAligner.align (0 ms) [----------] 1 test from SimpleAligner (0 ms total) [----------] Global test environment tear-down [==========] 1 test from 1 test suite ran. (0 ms total) [ PASSED ] 1 test. LD_LIBRARY_PATH=::::/usr/lib/aarch64-linux-gnu/hdf5/serial::: PBDAGCON_TEST_DATA_DIR=./ ./test-alngraph --gtest_output=xml:xml/test-alngraph.xml Running main() from /usr/src/googletest/googletest/src/gtest_main.cc [==========] Running 2 tests from 1 test suite. [----------] Global test environment set-up. [----------] 2 tests from AlnGraphBoostTest [ RUN ] AlnGraphBoostTest.RawConsensus [ OK ] AlnGraphBoostTest.RawConsensus (0 ms) [ RUN ] AlnGraphBoostTest.DanglingNodes [ OK ] AlnGraphBoostTest.DanglingNodes (0 ms) [----------] 2 tests from AlnGraphBoostTest (0 ms total) [----------] Global test environment tear-down [==========] 2 tests from 1 test suite ran. (0 ms total) [ PASSED ] 2 tests. make[2]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg/test/cpp' make[1]: Leaving directory '/build/pbdagcon-0.3+git20180411.c14c422+dfsg' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/pbdagcon/ dh_install dh_installdocs dh_installchangelogs dh_installexamples dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'pbdagcon-dbgsym' in '../pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_arm64.deb'. dpkg-deb: building package 'pbdagcon' in '../pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.deb'. dpkg-genbuildinfo --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo dpkg-genchanges --build=binary -O../pbdagcon_0.3+git20180411.c14c422+dfsg-8_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/17771 and its subdirectories I: Current time: Wed Apr 19 23:59:31 -12 2023 I: pbuilder-time-stamp: 1681991971 Thu Apr 20 11:59:34 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink15-arm64.debian.net. Thu Apr 20 11:59:34 UTC 2023 I: Preparing to do remote build '2' on codethink15-arm64.debian.net. Thu Apr 20 12:04:58 UTC 2023 I: Deleting $TMPDIR on codethink15-arm64.debian.net. Thu Apr 20 12:04:59 UTC 2023 I: pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.changes: Format: 1.8 Date: Thu, 10 Mar 2022 10:59:06 +0530 Source: pbdagcon Binary: pbdagcon pbdagcon-dbgsym Architecture: arm64 Version: 0.3+git20180411.c14c422+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Nilesh Patra Description: pbdagcon - sequence consensus using directed acyclic graphs Changes: pbdagcon (0.3+git20180411.c14c422+dfsg-8) unstable; urgency=medium . * Team Upload. * d/salsa-ci.yml: Disable reprotest * d/t/control: Versioned test dep on blasr Checksums-Sha1: cbf6819e9a6f6d63b950f1795ad4df77eab4516e 5923716 pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_arm64.deb ddf4720b6c4d520aa681b55524dfc114cfa6e39e 7411 pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo a3683d2586636fe11b668b3f691eb353327a51fd 321868 pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.deb Checksums-Sha256: 80c9fe2c56dbe00d3e6af07c6e576c3afc98eb6f7f69556140f47ae51b215422 5923716 pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_arm64.deb 680edce2282bf28c85bd88b364560d1f5f6ede4570f7ac1ef2ae6110ee01b693 7411 pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo 7214836adf3bded0d9fdc9bfc79af59a3436e5179fa01fc673f93770df6756c6 321868 pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.deb Files: 538ce1cfa9bce8e686de89ac9c4b9259 5923716 debug optional pbdagcon-dbgsym_0.3+git20180411.c14c422+dfsg-8_arm64.deb fa0f228d0643a5882b95d1fb52dd3381 7411 science optional pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo 0a52e042e397f8e5dcd7dccddf9e4c94 321868 science optional pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.deb Thu Apr 20 12:05:00 UTC 2023 I: diffoscope 240 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.AGdGy8JL/pbdagcon_0.3+git20180411.c14c422+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.AGdGy8JL/pbdagcon_0.3+git20180411.c14c422+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.AGdGy8JL/pbdagcon_0.3+git20180411.c14c422+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.AGdGy8JL/b1/pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.AGdGy8JL/b2/pbdagcon_0.3+git20180411.c14c422+dfsg-8_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: 0.749s) 0.749s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.143s) 0.142s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.001s) 0.001s 1 call specialize Thu Apr 20 12:05:18 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Thu Apr 20 12:05:18 UTC 2023 I: pbdagcon from bookworm built successfully and reproducibly on arm64. Thu Apr 20 12:05:21 UTC 2023 I: Submitting .buildinfo files to external archives: Thu Apr 20 12:05:21 UTC 2023 I: Submitting 12K b1/pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo.asc Thu Apr 20 12:05:22 UTC 2023 I: Submitting 12K b2/pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo.asc Thu Apr 20 12:05:23 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Thu Apr 20 12:05:23 UTC 2023 I: Done submitting .buildinfo files. Thu Apr 20 12:05:23 UTC 2023 I: Removing signed pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo.asc files: removed './b1/pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo.asc' removed './b2/pbdagcon_0.3+git20180411.c14c422+dfsg-8_arm64.buildinfo.asc'