Tue Aug 26 13:10:40 UTC 2025 I: starting to build ska/forky/arm64 on jenkins on '2025-08-26 13:10' Tue Aug 26 13:10:40 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_2/109927/console.log Tue Aug 26 13:10:40 UTC 2025 I: Downloading source for forky/ska=1.0+dfsg-6 --2025-08-26 13:10:40-- http://deb.debian.org/debian/pool/main/s/ska/ska_1.0%2bdfsg-6.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2028 (2.0K) [text/prs.lines.tag] Saving to: ‘ska_1.0+dfsg-6.dsc’ 0K . 100% 237M=0s 2025-08-26 13:10:40 (237 MB/s) - ‘ska_1.0+dfsg-6.dsc’ saved [2028/2028] Tue Aug 26 13:10:40 UTC 2025 I: ska_1.0+dfsg-6.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ska Binary: ska Architecture: any Version: 1.0+dfsg-6 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/simonrharris/SKA Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ska Vcs-Git: https://salsa.debian.org/med-team/ska.git Testsuite: autopkgtest Testsuite-Triggers: build-essential, googletest, libgtest-dev, zlib1g-dev Build-Depends: debhelper-compat (= 13), zlib1g-dev, googletest Package-List: ska deb science optional arch=any Checksums-Sha1: d5e6350fdb1968c91800d6b704495d54ecc0bfc4 85612 ska_1.0+dfsg.orig.tar.xz c1816d555ea40bb76024c2d414fcb3abfd7aad72 5328 ska_1.0+dfsg-6.debian.tar.xz Checksums-Sha256: 1a4aaa448c44b93010ee7dbacd4ff44dcd0876d6f4d9ed20a5ac5bf837e2ab42 85612 ska_1.0+dfsg.orig.tar.xz d81105999a671a2071324e9d0c1972c6e1b5872cee208dd2e5453a6bce419808 5328 ska_1.0+dfsg-6.debian.tar.xz Files: 6fc4064b3eef8153bee41ead25059339 85612 ska_1.0+dfsg.orig.tar.xz 014760c8a4984d8b24d8f5143ccff663 5328 ska_1.0+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJDBAEBCgAtFiEEy89k8fa3rclNjyokyeVeL63I9LkFAmiqZKkPHHNtckBkZWJp YW4ub3JnAAoJEMnlXi+tyPS5edQP/iH2bcwJ13aew3iU8lSfP6ETdDhHI/O7393T 76v2sA8QREIKU0Xlg2UOHy0hjlU9KhbEsQp7kymBW8ZUPF6qF4z+FWIG0HR7ltdK l+OChnoWYvK7pUZV2dktw75YVE5sQEWPr36io2aRqmhZlTC56kgo+LV/EBXLeCTy olJhh9DLxBod/jPOOzefvWioGyeiCtCwDvdlmO74QRw04utUcjkTDXPruH0VWbMv gcETrjR4r8p2pJJf0qxtZjQNTuD4CCzXnLAYsF5QMCcgwDdXjq1fY3BpHlP8Ytbz ml7odHpglg5IbRt9bkVDuQScigcxN03OpCVAgGb6uE3+2VsbaYGRNnwGL97PbrqH 6g0qStJ/QtMDExiF8cLnl8M0RZ4GJBc4++ct71fInhkCGN+nC7GdehzMhLgCz04W 0ryq8/aca0763E1ASV3kx5keBlbcF9QXXx9EtmtEnfhZztmQQSRTO2A4xcwdMY4B ZAO6qWsVQwgK0oaHCFN22mMaKH0JJV935hEAsxi5zrSqdjLHdHiipnzQ+IEAaDn4 btrpVvQhJbl3pdaI3Z0G3aB8EuDD4nj+8IIoaFtxjN6EEY0hHENypsEuY2QaDxtL DX2jU9RRAPvNwel48iuRwb42rJz2TfuQUSH4IImBa6kIw5lpEjUjwj2E/BuMm+Es FtLIooe7 =ENxa -----END PGP SIGNATURE----- Tue Aug 26 13:10:40 UTC 2025 I: Checking whether the package is not for us Tue Aug 26 13:10:40 UTC 2025 I: Starting 1st build on remote node codethink03-arm64.debian.net. Tue Aug 26 13:10:40 UTC 2025 I: Preparing to do remote build '1' on codethink03-arm64.debian.net. Tue Aug 26 13:12:33 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 28 07:33:41 -12 2026 I: pbuilder-time-stamp: 1790624021 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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 [ska_1.0+dfsg-6.dsc] I: copying [./ska_1.0+dfsg.orig.tar.xz] I: copying [./ska_1.0+dfsg-6.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ska_1.0+dfsg-6.dsc: no acceptable signature found dpkg-source: info: extracting ska in ska-1.0+dfsg dpkg-source: info: unpacking ska_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking ska_1.0+dfsg-6.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying include_vector.patch dpkg-source: info: applying 0002-Build-using-C-20.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2524748/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='forky' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='6a71c5ce03794ec2845ae5516d672787' 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='2524748' 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.xL8ooYmY/pbuilderrc_4vjZ --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/b1 --logfile b1/build.log ska_1.0+dfsg-6.dsc' SUDO_GID='109' SUDO_HOME='/var/lib/jenkins' 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 6.12.41+deb13-cloud-arm64 #1 SMP Debian 6.12.41-1 (2025-08-12) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2524748/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), zlib1g-dev, 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 ... 19969 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 zlib1g-dev; however: Package zlib1g-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} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libfile-stripnondeterminism-perl{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} po-debconf{a} sensible-utils{a} zlib1g-dev{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 12.4 MB of archives. After unpacking 49.6 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.1-1 [93.8 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.25 [91.6 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-4 [539 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 22 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.5+dfsg-0.1 [583 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 debhelper all 13.25 [937 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 googletest all 1.16.0-1 [517 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Fetched 12.4 MB in 0s (90.6 MB/s) Preconfiguring packages ... 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 ... 19969 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_arm64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.23.0-9_arm64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.41.1-1_arm64.deb ... Unpacking bsdextrautils (2.41.1-1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../08-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_arm64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.19-8_arm64.deb ... Unpacking m4 (1.4.19-8) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_13.25_all.deb ... Unpacking libdebhelper-perl (13.25) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-4_all.deb ... Unpacking libtool (2.5.4-4) ... 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 libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.14.1-2_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.1-2) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.14.1-2_all.deb ... Unpacking dh-strip-nondeterminism (1.14.1-2) ... Selecting previously unselected package libelf1t64:arm64. Preparing to unpack .../21-libelf1t64_0.192-4_arm64.deb ... Unpacking libelf1t64:arm64 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.15-1+b1_arm64.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package libunistring5:arm64. Preparing to unpack .../23-libunistring5_1.3-2_arm64.deb ... Unpacking libunistring5:arm64 (1.3-2) ... Selecting previously unselected package libxml2-16:arm64. Preparing to unpack .../24-libxml2-16_2.14.5+dfsg-0.1_arm64.deb ... Unpacking libxml2-16:arm64 (2.14.5+dfsg-0.1) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.23.1-2+b1_arm64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.25_all.deb ... Unpacking debhelper (13.25) ... Selecting previously unselected package googletest. Preparing to unpack .../29-googletest_1.16.0-1_all.deb ... Unpacking googletest (1.16.0-1) ... Selecting previously unselected package zlib1g-dev:arm64. Preparing to unpack .../30-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_arm64.deb ... Unpacking zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libpipeline1:arm64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-1) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:arm64 (2.14.5+dfsg-0.1) ... Setting up libdebhelper-perl (13.25) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up googletest (1.16.0-1) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.25) ... Processing triggers for libc-bin (2.41-12) ... 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/ska-1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../ska_1.0+dfsg-6_source.changes dpkg-buildpackage: info: source package ska dpkg-buildpackage: info: source version 1.0+dfsg-6 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steve M. Robbins dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_auto_clean make -j12 distclean make[1]: Entering directory '/build/reproducible-path/ska-1.0+dfsg' rm -f build/DNA.o build/general.o build/kmers.o build/sk_align.o build/sk_alleles.o build/sk_compare.o build/sk_distance.o build/sk_fasta.o build/sk_fastq.o build/sk_find.o build/sk_humanise.o build/sk_info.o build/sk_merge.o build/sk_refalign.o build/sk_summary.o build/sk_type.o build/sk_unique.o build/sk_weed.o build/ska.o rm -f bin/ska make[1]: Leaving directory '/build/reproducible-path/ska-1.0+dfsg' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure dh_auto_build make -j12 "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/ska-1.0+dfsg' g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/DNA.cpp -o build/DNA.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/general.cpp -o build/general.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/kmers.cpp -o build/kmers.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_align.cpp -o build/sk_align.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_alleles.cpp -o build/sk_alleles.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_compare.cpp -o build/sk_compare.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_distance.cpp -o build/sk_distance.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_fasta.cpp -o build/sk_fasta.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_fastq.cpp -o build/sk_fastq.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_find.cpp -o build/sk_find.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_humanise.cpp -o build/sk_humanise.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_info.cpp -o build/sk_info.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_merge.cpp -o build/sk_merge.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_refalign.cpp -o build/sk_refalign.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_summary.cpp -o build/sk_summary.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_type.cpp -o build/sk_type.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_unique.cpp -o build/sk_unique.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/sk_weed.cpp -o build/sk_weed.o g++ -g -std=c++20 -O2 -Isrc -Isrc -c src/ska.cpp -o build/ska.o g++ -g -std=c++20 -O2 -o bin/ska build/DNA.o build/general.o build/kmers.o build/sk_align.o build/sk_alleles.o build/sk_compare.o build/sk_distance.o build/sk_fasta.o build/sk_fastq.o build/sk_find.o build/sk_humanise.o build/sk_info.o build/sk_merge.o build/sk_refalign.o build/sk_summary.o build/sk_type.o build/sk_unique.o build/sk_weed.o build/ska.o -lz make[1]: Leaving directory '/build/reproducible-path/ska-1.0+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/ska-1.0+dfsg' cp -a tests tests.bak cd tests && ln -s /usr/src/googletest/googletest && make && \ ./general_unittest && ./kmers_unittest && ./DNA_unittest make[2]: Entering directory '/build/reproducible-path/ska-1.0+dfsg/tests' g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -c ../src//general.cpp ../src//general.cpp: In function ‘int openGzFileStream(const std::string&, igzstream&, bool)’: ../src//general.cpp:40:83: warning: unused parameter ‘verbose’ [-Wunused-parameter] 40 | int openGzFileStream(const std::string & fileName, igzstream & gzFileStream, bool verbose){ | ~~~~~^~~~~~~ g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -Igoogletest -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -c \ googletest/src/gtest-all.cc g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -Igoogletest -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -c \ googletest/src/gtest_main.cc ar -rv gtest_main.a gtest-all.o gtest_main.o ar: creating gtest_main.a a - gtest-all.o a - gtest_main.o g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -lpthread general.o general_unittest.cpp gtest_main.a -o general_unittest -lz g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -c ../src//kmers.cpp ../src//kmers.cpp: In function ‘int printKmerFile(const std::unordered_map, std::array >&, std::string, int, float)’: ../src//kmers.cpp:70:22: warning: unused variable ‘basefound’ [-Wunused-variable] 70 | bool basefound=false; | ^~~~~~~~~ ../src//kmers.cpp:75:22: warning: unused variable ‘maxbase’ [-Wunused-variable] 75 | char maxbase; | ^~~~~~~ ../src//kmers.cpp: In function ‘void addKmerToStringMap(std::unordered_map, std::__cxx11::basic_string >&, const std::string&, char, const std::vector&, const std::vector&, int, int, int)’: ../src//kmers.cpp:265:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 265 | for (int i=0; i::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 274 | for (int i=0; i, std::array >&, const int&)’: ../src//kmers.cpp:304:15: warning: unused variable ‘filecovcutoff’ [-Wunused-variable] 304 | float filecovcutoff; | ^~~~~~~~~~~~~ ../src//kmers.cpp: In function ‘int printKmerFile(const std::unordered_map, std::array >&, std::string, int, float)’: ../src//kmers.cpp:69:22: warning: ‘base’ may be used uninitialized [-Wmaybe-uninitialized] 69 | char base; | ^~~~ g++ -std=c++20 -Wdate-time -D_FORTIFY_SOURCE=2 -isystem googletest/include -g -O2 -ffile-prefix-map=/build/reproducible-path/ska-1.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -g -Wall -Wextra -pthread -c ../src//DNA.cpp ../src//DNA.cpp: In function ‘int circulariseSequence(std::string&, int)’: ../src//DNA.cpp:187:32: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 187 | if (mySequence.length() Changed-By: Steve M. Robbins Description: ska - Split Kmer Analysis Changes: ska (1.0+dfsg-6) unstable; urgency=medium . * [115f0f6] Fix autopkgtests: remove -std++14 since googletest now supports C++17 and above. Checksums-Sha1: 2d27038c76cf0186289c7dd6aafb781206ab2789 2507188 ska-dbgsym_1.0+dfsg-6_arm64.deb fc3afe1afdd6e3dc4fae75679f239bd7029ea54e 4919 ska_1.0+dfsg-6_arm64.buildinfo 22d4aadf68907fa5dbac1018d372a706e0aedf9a 142908 ska_1.0+dfsg-6_arm64.deb Checksums-Sha256: 84828cc02ea5eb2dabef85a5b51465605a5451a11525e3c018d62d42f0f411b1 2507188 ska-dbgsym_1.0+dfsg-6_arm64.deb d81f408c0c60745c7afcb32dbd588418ed74026e057ae7c3392c44559b2c0010 4919 ska_1.0+dfsg-6_arm64.buildinfo 2a8e68719199ee6328153e6c084239882e46c366fcb44af7bfff94ecfd9d1c58 142908 ska_1.0+dfsg-6_arm64.deb Files: 3c81f0782e292465b3d0b2278f6990ba 2507188 debug optional ska-dbgsym_1.0+dfsg-6_arm64.deb c168aa0f6be9434faa9d06bef38dd42f 4919 science optional ska_1.0+dfsg-6_arm64.buildinfo df4e262c565d3918aec0c1197ffaa32e 142908 science optional ska_1.0+dfsg-6_arm64.deb Tue Aug 26 13:14:19 UTC 2025 I: diffoscope 305 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_2-109927.service; invocation ID: 4b8e14e732cd460886ab9f46a3778f64 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/ska_1.0+dfsg-6.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/ska_1.0+dfsg-6.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/ska_1.0+dfsg-6.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/b1/ska_1.0+dfsg-6_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.xL8ooYmY/b2/ska_1.0+dfsg-6_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 diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 208ms CPU time consumed: 170ms Memory peak: 18M (swap: 0B) Tue Aug 26 13:14:20 UTC 2025 I: diffoscope 305 found no differences in the changes files, and a .buildinfo file also exists. Tue Aug 26 13:14:20 UTC 2025 I: ska from forky built successfully and reproducibly on arm64. Tue Aug 26 13:14:20 UTC 2025 I: Removing signed ska_1.0+dfsg-6_arm64.buildinfo.asc files: removed './b1/ska_1.0+dfsg-6_arm64.buildinfo.asc' removed './b2/ska_1.0+dfsg-6_arm64.buildinfo.asc'