Wed Apr 12 19:59:34 UTC 2023 I: starting to build kraken/bookworm/arm64 on jenkins on '2023-04-12 19:59' Wed Apr 12 19:59:34 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_31/9085/console.log Wed Apr 12 19:59:34 UTC 2023 I: Downloading source for bookworm/kraken=1.1.1-4 --2023-04-12 19:59:34-- http://cdn-fastly.deb.debian.org/debian/pool/main/k/kraken/kraken_1.1.1-4.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 1953 (1.9K) [text/prs.lines.tag] Saving to: ‘kraken_1.1.1-4.dsc’ 0K . 100% 119M=0s 2023-04-12 19:59:34 (119 MB/s) - ‘kraken_1.1.1-4.dsc’ saved [1953/1953] Wed Apr 12 19:59:34 UTC 2023 I: kraken_1.1.1-4.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: kraken Binary: kraken Architecture: any Version: 1.1.1-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://ccb.jhu.edu/software/kraken/ Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/kraken Vcs-Git: https://salsa.debian.org/med-team/kraken.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), jellyfish1 Package-List: kraken deb science optional arch=any Checksums-Sha1: 56e70d9b6a9d90bdabfb76f6bd5c14bb92f7bd82 76541 kraken_1.1.1.orig.tar.gz e44a12a51c7affa05d7605fc38bd6981e069d8b0 337236 kraken_1.1.1-4.debian.tar.xz Checksums-Sha256: 73e48f40418f92b8cf036ca1da727ca3941da9b78d4c285b81ba3267326ac4ee 76541 kraken_1.1.1.orig.tar.gz b3adb7c91b18d79310d4610d15df87c875ad4a5ec0db7ef90fa7072f7fb0f00e 337236 kraken_1.1.1-4.debian.tar.xz Files: 91b988e05ffaa128c7bf28816a41a910 76541 kraken_1.1.1.orig.tar.gz 59fcafd28b74c88dacd83b1a76cb4d20 337236 kraken_1.1.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmNm0K0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFBWRAAiiTM5dOVYShdnRiH8LSmszuMSvm+6XsL /sOkULU6QfXyFpiHL6liqUmPSBTQC+PxsisRV+2DGroIjbwyX2YKIMkVKwh0Mvug 3Xzu2/3MXf1BJtu0d9hrcbnFNSCEuExG7lcGoK3dzUHgw3AS5QeCt934jRUcRlWz 7luAtVvExWQXoG78xs/zEu+2y1P+XPF1diooDlc6TMBHykq3pLultqxnY4bwG4gn ZzZFSP7qsX6LjN8ON9lLYt08Da01gVtOJMXEeQRynqZUx0vrnCLAwyVXX8R6lxrF C8JmbE9YwBIb0dagDRIeNSA8tfgTGfnf4k1cMwNM+uK4jbBklA1nS7y2i3r2JyGt YPK5caZreQSu/yzzHV1vDiicY9BqWGYKFF2OjpRn7boaeZE7yu6sKPsJLIqsc8y0 c7fjTiyq41gb24/OqVqeTD7anfR9K9Z6JjJRPoJnnJBScGF1KHrGWau92XDOQXy1 Xq2vTP9d0F5fpGWUYct06lLwDIYzW8TyY/pyqLu1ZKtq+iqBHWjPPL32lEUohJJR xzteDtAPBtgK2zmL+T0i3qJDTxvihaHJkGYwfK+vwKRlDBPOjK9Hlrhr7KJkYJ75 EaeGKh8z6IeIGiXnJCGNqCvCNTOXrEzdQZoXLlqjSaIjj+TQlhkhaAQtTffVFX1t vhiXp1Vx4Q4= =ke2l -----END PGP SIGNATURE----- Wed Apr 12 19:59:34 UTC 2023 I: Checking whether the package is not for us Wed Apr 12 19:59:34 UTC 2023 I: Starting 1st build on remote node codethink16-arm64.debian.net. Wed Apr 12 19:59:34 UTC 2023 I: Preparing to do remote build '1' on codethink16-arm64.debian.net. Wed Apr 12 20:01:26 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Wed Apr 12 07:59:39 -12 2023 I: pbuilder-time-stamp: 1681329579 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 [kraken_1.1.1-4.dsc] I: copying [./kraken_1.1.1.orig.tar.gz] I: copying [./kraken_1.1.1-4.debian.tar.xz] I: Extracting source gpgv: Signature made Sat Nov 5 09:07:57 2022 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./kraken_1.1.1-4.dsc: no acceptable signature found dpkg-source: info: extracting kraken in kraken-1.1.1 dpkg-source: info: unpacking kraken_1.1.1.orig.tar.gz dpkg-source: info: unpacking kraken_1.1.1-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_jellyfish1.patch dpkg-source: info: applying kraken_tmp_dir.patch dpkg-source: info: applying fix_reading_fasta.patch dpkg-source: info: applying hardening.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25328/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='25328' 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.PuID0PFY/pbuilderrc_RSYb --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.PuID0PFY/b1 --logfile b1/build.log kraken_1.1.1-4.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 codethink16-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 10 22:26 /bin -> usr/bin I: user script /srv/workspace/pbuilder/25328/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), jellyfish1 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 jellyfish1; however: Package jellyfish1 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} jellyfish1{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 31 newly installed, 0 to remove and 0 not upgraded. Need to get 18.5 MB of archives. After unpacking 75.1 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 11 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 21 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 jellyfish1 arm64 1.1.11-8 [130 kB] Fetched 18.5 MB in 1s (15.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package sensible-utils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../02-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../19-libsub-override-perl_0.09-4_all.deb ... Unpacking libsub-override-perl (0.09-4) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../20-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../21-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../22-libelf1_0.188-2.1_arm64.deb ... Unpacking libelf1:arm64 (0.188-2.1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.1+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-12_arm64.deb ... Unpacking gettext (0.21-12) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../27-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../28-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../29-debhelper_13.11.4_all.deb ... Unpacking debhelper (13.11.4) ... Selecting previously unselected package jellyfish1. Preparing to unpack .../30-jellyfish1_1.1.11-8_arm64.deb ... Unpacking jellyfish1 (1.1.11-8) ... Setting up libpipeline1:arm64 (1.5.7-1) ... Setting up libicu72:arm64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up jellyfish1 (1.1.11-8) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-12) ... Setting up autoconf (2.71-3) ... 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 libelf1:arm64 (0.188-2.1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.1+b3) ... 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 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 po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.11.4) ... Processing triggers for libc-bin (2.36-8) ... 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/kraken-1.1.1/ && 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 > ../kraken_1.1.1-4_source.changes dpkg-buildpackage: info: source package kraken dpkg-buildpackage: info: source version 1.1.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --sourcedirectory=src dh_auto_clean -O--sourcedirectory=src cd src && make -j8 clean make[1]: Entering directory '/build/kraken-1.1.1/src' rm -f db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator *.o make[1]: Leaving directory '/build/kraken-1.1.1/src' dh_autoreconf_clean -O--sourcedirectory=src dh_clean -O--sourcedirectory=src debian/rules binary dh binary --sourcedirectory=src dh_update_autotools_config -O--sourcedirectory=src dh_autoreconf -O--sourcedirectory=src dh_auto_configure -O--sourcedirectory=src dh_auto_build -O--sourcedirectory=src cd src && make -j8 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/kraken-1.1.1/src' g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -c krakendb.cpp g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -c quickfile.cpp g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -c krakenutil.cpp g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -c seqreader.cpp g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now make_seqid_to_taxid_map.cpp quickfile.o -o make_seqid_to_taxid_map g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now db_sort.cpp krakendb.o quickfile.o -o db_sort g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now db_shrink.cpp krakendb.o quickfile.o -o db_shrink g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now set_lcas.cpp krakendb.o quickfile.o krakenutil.o seqreader.o -o set_lcas g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now classify.cpp krakendb.o quickfile.o krakenutil.o seqreader.o -o classify g++ -g -O2 -ffile-prefix-map=/build/kraken-1.1.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -fopenmp -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now kmer_estimator.cpp krakenutil.o seqreader.o -o kmer_estimator db_shrink.cpp: In function 'int main(int, char**)': db_shrink.cpp:55:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 55 | delete buffer; | ^~~~~~ db_shrink.cpp:46:28: note: returned from 'void* operator new [](std::size_t)' 46 | char *buffer = new char[8]; | ^ db_shrink.cpp:79:10: warning: 'void operator delete(void*, std::size_t)' called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 79 | delete buffer; | ^~~~~~ db_shrink.cpp:58:32: note: returned from 'void* operator new [](std::size_t)' 58 | buffer = new char[header_size]; | ^ make[1]: Leaving directory '/build/kraken-1.1.1/src' dh_auto_test -O--sourcedirectory=src create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=src dh_prep -O--sourcedirectory=src dh_installdirs -O--sourcedirectory=src debian/rules override_dh_auto_install make[1]: Entering directory '/build/kraken-1.1.1' dh_auto_install -- KRAKEN_DIR=/build/kraken-1.1.1/debian/kraken/usr/lib/kraken cd src && make -j8 install DESTDIR=/build/kraken-1.1.1/debian/kraken AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" KRAKEN_DIR=/build/kraken-1.1.1/debian/kraken/usr/lib/kraken make[2]: Entering directory '/build/kraken-1.1.1/src' cp db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator /build/kraken-1.1.1/debian/kraken/usr/lib/kraken/ make[2]: Leaving directory '/build/kraken-1.1.1/src' ./install_kraken.sh /usr/lib/kraken kraken make[1]: Leaving directory '/build/kraken-1.1.1' debian/rules override_dh_install make[1]: Entering directory '/build/kraken-1.1.1' dh_install for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done make[1]: Leaving directory '/build/kraken-1.1.1' dh_installdocs -O--sourcedirectory=src dh_installchangelogs -O--sourcedirectory=src dh_installman -O--sourcedirectory=src dh_installsystemduser -O--sourcedirectory=src dh_perl -O--sourcedirectory=src debian/rules override_dh_link make[1]: Entering directory '/build/kraken-1.1.1' dh_link for file in /build/kraken-1.1.1/debian/kraken/usr/lib/kraken/kraken* ; do \ if ! echo ${file} | grep -q '\.pm$' ; then \ ln -s ../lib/kraken/`basename ${file}` /build/kraken-1.1.1/debian/kraken/usr/bin/`basename ${file}` ; \ fi \ done make[1]: Leaving directory '/build/kraken-1.1.1' dh_strip_nondeterminism -O--sourcedirectory=src dh_compress -O--sourcedirectory=src dh_fixperms -O--sourcedirectory=src dh_missing -O--sourcedirectory=src dh_dwz -a -O--sourcedirectory=src dh_strip -a -O--sourcedirectory=src dh_makeshlibs -a -O--sourcedirectory=src dh_shlibdeps -a -O--sourcedirectory=src dh_installdeb -O--sourcedirectory=src dh_gencontrol -O--sourcedirectory=src dpkg-gencontrol: warning: package kraken: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package kraken: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=src dh_builddeb -O--sourcedirectory=src dpkg-deb: building package 'kraken' in '../kraken_1.1.1-4_arm64.deb'. dpkg-deb: building package 'kraken-dbgsym' in '../kraken-dbgsym_1.1.1-4_arm64.deb'. dpkg-genbuildinfo --build=binary -O../kraken_1.1.1-4_arm64.buildinfo dpkg-genchanges --build=binary -O../kraken_1.1.1-4_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/25328 and its subdirectories I: Current time: Wed Apr 12 08:01:24 -12 2023 I: pbuilder-time-stamp: 1681329684 Wed Apr 12 20:01:26 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink13-arm64.debian.net. Wed Apr 12 20:01:26 UTC 2023 I: Preparing to do remote build '2' on codethink13-arm64.debian.net. Wed Apr 12 20:03:06 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net. Wed Apr 12 20:03:07 UTC 2023 I: kraken_1.1.1-4_arm64.changes: Format: 1.8 Date: Sat, 05 Nov 2022 21:58:35 +0100 Source: kraken Binary: kraken kraken-dbgsym Architecture: arm64 Version: 1.1.1-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: kraken - assigning taxonomic labels to short DNA sequences Changes: kraken (1.1.1-4) unstable; urgency=medium . * Fix watch file * Standards-Version: 4.6.1 (routine-update) * lintian-overrides (see lintian bug #1017966) Checksums-Sha1: e6f0d88230c9ebd1499f5206e9097040ec4f95c9 887504 kraken-dbgsym_1.1.1-4_arm64.deb f649d75e596523cda29138f8b6462bdbe27da8c2 5135 kraken_1.1.1-4_arm64.buildinfo 37eaf7b3f2ca97a7b759c72fe9e2ab5bfe66fbc1 746608 kraken_1.1.1-4_arm64.deb Checksums-Sha256: 3554eb15c337910e34d2a33e6df9b712f2b5346d30bfcdbe51b5dd8bb533b2f3 887504 kraken-dbgsym_1.1.1-4_arm64.deb d047a34164052f5f76bb4a3852e9c98bb5e5521bea7f4b6d5966201d4d3267a7 5135 kraken_1.1.1-4_arm64.buildinfo 2e90b1647c759ab070e00213227aae80408838d6e1ce88236430c47f9e7f6878 746608 kraken_1.1.1-4_arm64.deb Files: afb62802180aab116c3ef2b5c1fcd83d 887504 debug optional kraken-dbgsym_1.1.1-4_arm64.deb 7f6b1eb3acda6902f25c3324fcf6e554 5135 science optional kraken_1.1.1-4_arm64.buildinfo 51a6913650e5aca569c96e82db807502 746608 science optional kraken_1.1.1-4_arm64.deb Wed Apr 12 20:03:09 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.PuID0PFY/kraken_1.1.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.PuID0PFY/kraken_1.1.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.PuID0PFY/kraken_1.1.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.PuID0PFY/b1/kraken_1.1.1-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.PuID0PFY/b2/kraken_1.1.1-4_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: 0.408s) 0.408s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.033s) 0.033s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Wed Apr 12 20:03:10 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Wed Apr 12 20:03:10 UTC 2023 I: kraken from bookworm built successfully and reproducibly on arm64. Wed Apr 12 20:03:12 UTC 2023 I: Submitting .buildinfo files to external archives: Wed Apr 12 20:03:12 UTC 2023 I: Submitting 8.0K b1/kraken_1.1.1-4_arm64.buildinfo.asc Wed Apr 12 20:03:14 UTC 2023 I: Submitting 8.0K b2/kraken_1.1.1-4_arm64.buildinfo.asc Wed Apr 12 20:03:15 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed Apr 12 20:03:15 UTC 2023 I: Done submitting .buildinfo files. Wed Apr 12 20:03:15 UTC 2023 I: Removing signed kraken_1.1.1-4_arm64.buildinfo.asc files: removed './b1/kraken_1.1.1-4_arm64.buildinfo.asc' removed './b2/kraken_1.1.1-4_arm64.buildinfo.asc'