Wed May 8 20:58:10 UTC 2024 I: starting to build kraken/unstable/arm64 on jenkins on '2024-05-08 20:57' Wed May 8 20:58:10 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_23/40259/console.log Wed May 8 20:58:10 UTC 2024 I: Downloading source for unstable/kraken=1.1.1-4 --2024-05-08 20:58:11-- http://deb.debian.org/debian/pool/main/k/kraken/kraken_1.1.1-4.dsc Connecting to 46.16.76.132:3128... 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% 298M=0s 2024-05-08 20:58:11 (298 MB/s) - ‘kraken_1.1.1-4.dsc’ saved [1953/1953] Wed May 8 20:58:11 UTC 2024 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 May 8 20:58:11 UTC 2024 I: Checking whether the package is not for us Wed May 8 20:58:11 UTC 2024 I: Starting 1st build on remote node codethink03-arm64.debian.net. Wed May 8 20:58:11 UTC 2024 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Wed May 8 20:59:19 UTC 2024 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Jun 10 15:21:13 -12 2025 I: pbuilder-time-stamp: 1749612073 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 21:07:57 2022 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/3445267/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='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='59d011a683b440218214c7524bbd1a5b' 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='3445267' 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.us74ec0U/pbuilderrc_8IQG --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/b1 --logfile b1/build.log kraken_1.1.1-4.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 codethink03-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 Jun 9 14:06 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3445267/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 ... 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 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} libelf1t64{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1t64{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 18.8 MB of archives. After unpacking 76.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-4 [1130 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 23 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 jellyfish1 arm64 1.1.11-9 [130 kB] Fetched 18.8 MB in 0s (64.3 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 ... 19744 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_arm64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_arm64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-4_arm64.deb ... Unpacking groff-base (1.23.0-4) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.40-8_arm64.deb ... Unpacking bsdextrautils (2.40-8) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.7-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-2) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.12.1-1_arm64.deb ... Unpacking man-db (2.12.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... 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_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.15.3_all.deb ... Unpacking libdebhelper-perl (13.15.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... 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_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... 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 libelf1t64:arm64. Preparing to unpack .../22-libelf1t64_0.191-1+b1_arm64.deb ... Unpacking libelf1t64:arm64 (0.191-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../23-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../24-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../25-libxml2_2.9.14+dfsg-1.3+b3_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b3) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... 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_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package jellyfish1. Preparing to unpack .../30-jellyfish1_1.1.11-9_arm64.deb ... Unpacking jellyfish1 (1.1.11-9) ... Setting up libpipeline1:arm64 (1.5.7-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.40-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:arm64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libelf1t64:arm64 (0.191-1+b1) ... Setting up jellyfish1 (1.1.11-9) ... Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+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 (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... 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 groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Processing triggers for libc-bin (2.38-8) ... 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/reproducible-path/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 -j12 clean make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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 -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/kraken-1.1.1/src' g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -fopenmp -O3 -c krakendb.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -fopenmp -O3 -c quickfile.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -fopenmp -O3 -c krakenutil.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wall -fopenmp -O3 -c seqreader.cpp g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 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]; | ^ g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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/reproducible-path/kraken-1.1.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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 make[1]: Leaving directory '/build/reproducible-path/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/reproducible-path/kraken-1.1.1' dh_auto_install -- KRAKEN_DIR=/build/reproducible-path/kraken-1.1.1/debian/kraken/usr/lib/kraken cd src && make -j12 install DESTDIR=/build/reproducible-path/kraken-1.1.1/debian/kraken AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" KRAKEN_DIR=/build/reproducible-path/kraken-1.1.1/debian/kraken/usr/lib/kraken make[2]: Entering directory '/build/reproducible-path/kraken-1.1.1/src' cp db_sort set_lcas classify make_seqid_to_taxid_map db_shrink kmer_estimator /build/reproducible-path/kraken-1.1.1/debian/kraken/usr/lib/kraken/ make[2]: Leaving directory '/build/reproducible-path/kraken-1.1.1/src' ./install_kraken.sh /usr/lib/kraken kraken make[1]: Leaving directory '/build/reproducible-path/kraken-1.1.1' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/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/reproducible-path/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/reproducible-path/kraken-1.1.1' dh_link for file in /build/reproducible-path/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/reproducible-path/kraken-1.1.1/debian/kraken/usr/bin/`basename ${file}` ; \ fi \ done make[1]: Leaving directory '/build/reproducible-path/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/3445267 and its subdirectories I: Current time: Tue Jun 10 15:22:17 -12 2025 I: pbuilder-time-stamp: 1749612137 Wed May 8 20:59:19 UTC 2024 I: 1st build successful. Starting 2nd build on remote node codethink04-arm64.debian.net. Wed May 8 20:59:19 UTC 2024 I: Preparing to do remote build '2' on codethink04-arm64.debian.net. Wed May 8 21:00:35 UTC 2024 I: Deleting $TMPDIR on codethink04-arm64.debian.net. Wed May 8 21:00:36 UTC 2024 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: 9291c96104c94a20fc9ed38adb7c74d63e95692d 855840 kraken-dbgsym_1.1.1-4_arm64.deb 1c928221a94d732a84d2fe65e7f0f1e3d0e4c5ae 5099 kraken_1.1.1-4_arm64.buildinfo 83a5b9d0c02cb5fe94a752a1fd4254b96b257367 747108 kraken_1.1.1-4_arm64.deb Checksums-Sha256: 1061c638bcd4d7a7fff6e45c88cad39354a2cdc85a342977086875130947b755 855840 kraken-dbgsym_1.1.1-4_arm64.deb 31380acc47d441e8281e37139da180884455ebf3240acb523289521031006634 5099 kraken_1.1.1-4_arm64.buildinfo 50485f17977514c8986ef4baf7660a1c9a5dc327aa8870f849cfe60d26f8abe4 747108 kraken_1.1.1-4_arm64.deb Files: 72bd45b922e0c7927f6cc8e704651833 855840 debug optional kraken-dbgsym_1.1.1-4_arm64.deb afd38d19c8f58ce3601bbbdfe9a4b335 5099 science optional kraken_1.1.1-4_arm64.buildinfo 38eba4f617c0bde2298f4856b0b1b0e1 747108 science optional kraken_1.1.1-4_arm64.deb Wed May 8 21:00:37 UTC 2024 I: diffoscope 265 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_23-40259.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/kraken_1.1.1-4.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/kraken_1.1.1-4.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/kraken_1.1.1-4.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/b1/kraken_1.1.1-4_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.us74ec0U/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: 0.397s) 0.397s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.045s) 0.045s 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: 744ms CPU time consumed: 731ms Wed May 8 21:00:38 UTC 2024 I: diffoscope 265 found no differences in the changes files, and a .buildinfo file also exists. Wed May 8 21:00:38 UTC 2024 I: kraken from unstable built successfully and reproducibly on arm64. Wed May 8 21:00:40 UTC 2024 I: Submitting .buildinfo files to external archives: Wed May 8 21:00:40 UTC 2024 I: Submitting 8.0K b1/kraken_1.1.1-4_arm64.buildinfo.asc Wed May 8 21:00:41 UTC 2024 I: Submitting 8.0K b2/kraken_1.1.1-4_arm64.buildinfo.asc Wed May 8 21:00:43 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Wed May 8 21:00:43 UTC 2024 I: Done submitting .buildinfo files. Wed May 8 21:00:43 UTC 2024 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'