Mon Oct 20 07:00:46 UTC 2025 I: starting to build srst2/forky/arm64 on jenkins on '2025-10-20 07:00' Mon Oct 20 07:00:46 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/125615/console.log Mon Oct 20 07:00:46 UTC 2025 I: Downloading source for forky/srst2=0.2.0-13 --2025-10-20 07:00:46-- http://deb.debian.org/debian/pool/main/s/srst2/srst2_0.2.0-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2269 (2.2K) [text/prs.lines.tag] Saving to: ‘srst2_0.2.0-13.dsc’ 0K .. 100% 250M=0s 2025-10-20 07:00:46 (250 MB/s) - ‘srst2_0.2.0-13.dsc’ saved [2269/2269] Mon Oct 20 07:00:46 UTC 2025 I: srst2_0.2.0-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: srst2 Binary: srst2 Architecture: any Version: 0.2.0-13 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Étienne Mollier Homepage: https://katholt.github.io/srst2/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/srst2 Vcs-Git: https://salsa.debian.org/med-team/srst2.git Testsuite: autopkgtest Testsuite-Triggers: python3-mock Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3, python3-setuptools, discount , dos2unix, python3-scipy , bowtie2 , samtools Package-List: srst2 deb science optional arch=any Checksums-Sha1: b10c53e3a16271e4506ce253200410884b02679a 1380071 srst2_0.2.0.orig.tar.gz 0214122734d772d823ed3c9873abf0475b02665e 18620 srst2_0.2.0-13.debian.tar.xz Checksums-Sha256: 352c59bdf00039dfa5610a4b88049a0eb114d7c2a305d4924b6e605cc6d15123 1380071 srst2_0.2.0.orig.tar.gz 3ded0806794198fc0bc27628677eb5cab6640c1ab2f46c2b3ee8a78934f28a32 18620 srst2_0.2.0-13.debian.tar.xz Files: ef447fc394d2f60adc2a32edd6ebe374 1380071 srst2_0.2.0.orig.tar.gz 0d13aaa2dca9371e907ca792ee800ef9 18620 srst2_0.2.0-13.debian.tar.xz Dgit: f1820320070fdd839c148a0561f39b9455671ce0 debian archive/debian/0.2.0-13 https://git.dgit.debian.org/srst2 -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmdSIJcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdruOQ//WBlAVcfc0kis9t/jbxqqick6Eoad jEnMKXzNJlylZGYrJDGSVFp7PK1tRYytlzvybKrqr/yYOZ2Fcp7CjtGxbuVyMtPf DZLTVFpFFBETs2d9NWCpBEHZkoMcOqx3q51+dtYBJhcm5ibb9KKcvCG0Yz4ZXL69 inUfCX5Bss+bIV3n1xqayedCwrmjv3acdXrIwYxORtWjh3IzK+IRdLxlE2TuJLOK HWQx3jrKfmbBZ13VhvIhRW1mumoRezsEnashXlo4ajvI1CEadZqEgdArTLcP+ERq /tAQELY4zBkyk8p6pOxCch5TS9cc/TQTD3sfwEhSs+PKutAj4hU8FVpEgGcpnWiQ NYnzAOMGH0rTrRaVmBu9wQWsM51raSsBo6HwikQMJn21z42xhMFsLBxuO6cHM9GC kE3IWOz8L/x5Y4nhoBV8Bw+ItzRL19hmmb/v13yMwyRsHVl5cYeBPJJlBFHbq14o Kb5WO84Ipr8tAE5Wc92FxtkqBGL+BeQyjYR3sF8ngj+aMVdy/sgqXXVVRlLtnxXI KXqMzMKw1cfdrLvcIXpzOuJJ31S+BOGpm1os0QO/RtrSWtpr67YT42Takc7oepWX G/Bq2BACqJew3SP9ybd/mxXom6qO1h/sn+UDoMPYAXvmTOOEyk4+fDbsue/Ep8k3 E8SZND98TRU7fmM= =nOzf -----END PGP SIGNATURE----- Mon Oct 20 07:00:46 UTC 2025 I: Checking whether the package is not for us Mon Oct 20 07:00:46 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Mon Oct 20 07:00:46 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Mon Oct 20 07:01:38 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Oct 19 19:00:48 -12 2025 I: pbuilder-time-stamp: 1760943648 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 [srst2_0.2.0-13.dsc] I: copying [./srst2_0.2.0.orig.tar.gz] I: copying [./srst2_0.2.0-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./srst2_0.2.0-13.dsc: no acceptable signature found dpkg-source: info: extracting srst2 in srst2-0.2.0 dpkg-source: info: unpacking srst2_0.2.0.orig.tar.gz dpkg-source: info: unpacking srst2_0.2.0-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying check_command_line_arguments.patch dpkg-source: info: applying add_usr_bin_python_to_scripts.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying fix_grep_call.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying biopython-1.78.patch dpkg-source: info: applying syntax-warning.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/901986/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='f16d173a8ebc418593e243a96bee7d29' 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='901986' 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.VpKMndip/pbuilderrc_oS0r --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.VpKMndip/b1 --logfile b1/build.log srst2_0.2.0-13.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 codethink04-arm64 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/901986/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), dh-sequence-python3, python3, python3-setuptools, discount, dos2unix, python3-scipy, bowtie2, samtools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 20000 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 dh-sequence-python3; however: Package dh-sequence-python3 is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on discount; however: Package discount is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on bowtie2; however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on samtools; however: Package samtools 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} bowtie2{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} discount{a} dos2unix{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libcom-err2{a} libcurl3t64-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhts3t64{a} libhtscodecs2{a} libidn2-0{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libmarkdown2{a} libncurses6{a} libnghttp2-14{a} libnghttp3-9{a} libngtcp2-16{a} libngtcp2-crypto-gnutls8{a} libp11-kit0{a} libpipeline1{a} libpsl5t64{a} libpython3-stdlib{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2-16{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-decorator{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-numpy{a} python3-numpy-dev{a} python3-pkg-resources{a} python3-scipy{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-minimal{a} readline-common{a} samtools{a} sensible-utils{a} tzdata{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix python3-pil python3-pooch python3-yaml wget 0 packages upgraded, 93 newly installed, 0 to remove and 0 not upgraded. Need to get 47.3 MB of archives. After unpacking 209 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main arm64 libexpat1 arm64 2.7.3-1 [96.5 kB] Get: 2 http://deb.debian.org/debian forky/main arm64 libpython3.13-minimal arm64 3.13.8-1 [858 kB] Get: 3 http://deb.debian.org/debian forky/main arm64 python3.13-minimal arm64 3.13.8-1 [2062 kB] Get: 4 http://deb.debian.org/debian forky/main arm64 python3-minimal arm64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian forky/main arm64 media-types all 14.0.0 [30.8 kB] Get: 6 http://deb.debian.org/debian forky/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian forky/main arm64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian forky/main arm64 libffi8 arm64 3.5.2-2 [21.5 kB] Get: 9 http://deb.debian.org/debian forky/main arm64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian forky/main arm64 libreadline8t64 arm64 8.3-3 [169 kB] Get: 11 http://deb.debian.org/debian forky/main arm64 libpython3.13-stdlib arm64 3.13.8-1 [1899 kB] Get: 12 http://deb.debian.org/debian forky/main arm64 python3.13 arm64 3.13.8-1 [765 kB] Get: 13 http://deb.debian.org/debian forky/main arm64 libpython3-stdlib arm64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian forky/main arm64 python3 arm64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian forky/main arm64 python3-numpy-dev arm64 1:2.2.4+ds-1.2 [138 kB] Get: 16 http://deb.debian.org/debian forky/main arm64 libblas3 arm64 3.12.1-7 [135 kB] Get: 17 http://deb.debian.org/debian forky/main arm64 libgfortran5 arm64 15.2.0-4 [371 kB] Get: 18 http://deb.debian.org/debian forky/main arm64 liblapack3 arm64 3.12.1-7 [1846 kB] Get: 19 http://deb.debian.org/debian forky/main arm64 python3-numpy arm64 1:2.2.4+ds-1.2 [3620 kB] Get: 20 http://deb.debian.org/debian forky/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get: 21 http://deb.debian.org/debian forky/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 22 http://deb.debian.org/debian forky/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 23 http://deb.debian.org/debian forky/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 24 http://deb.debian.org/debian forky/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB] Get: 25 http://deb.debian.org/debian forky/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB] Get: 26 http://deb.debian.org/debian forky/main arm64 groff-base arm64 1.23.0-9 [1130 kB] Get: 27 http://deb.debian.org/debian forky/main arm64 bsdextrautils arm64 2.41.2-1 [94.3 kB] Get: 28 http://deb.debian.org/debian forky/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 29 http://deb.debian.org/debian forky/main arm64 man-db arm64 2.13.1-1 [1453 kB] Get: 30 http://deb.debian.org/debian forky/main arm64 m4 arm64 1.4.20-2 [315 kB] Get: 31 http://deb.debian.org/debian forky/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 32 http://deb.debian.org/debian forky/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 33 http://deb.debian.org/debian forky/main arm64 automake all 1:1.17-4 [862 kB] Get: 34 http://deb.debian.org/debian forky/main arm64 autopoint all 0.23.1-2 [770 kB] Get: 35 http://deb.debian.org/debian forky/main arm64 bowtie2 arm64 2.5.4-1+b2 [1399 kB] Get: 36 http://deb.debian.org/debian forky/main arm64 libdebhelper-perl all 13.28 [92.4 kB] Get: 37 http://deb.debian.org/debian forky/main arm64 libtool all 2.5.4-5 [540 kB] Get: 38 http://deb.debian.org/debian forky/main arm64 dh-autoreconf all 21 [12.2 kB] Get: 39 http://deb.debian.org/debian forky/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian forky/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 41 http://deb.debian.org/debian forky/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 42 http://deb.debian.org/debian forky/main arm64 libelf1t64 arm64 0.193-3 [189 kB] Get: 43 http://deb.debian.org/debian forky/main arm64 dwz arm64 0.16-2 [100 kB] Get: 44 http://deb.debian.org/debian forky/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 45 http://deb.debian.org/debian forky/main arm64 libxml2-16 arm64 2.14.6+dfsg-0.1 [601 kB] Get: 46 http://deb.debian.org/debian forky/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB] Get: 47 http://deb.debian.org/debian forky/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 48 http://deb.debian.org/debian forky/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 49 http://deb.debian.org/debian forky/main arm64 debhelper all 13.28 [941 kB] Get: 50 http://deb.debian.org/debian forky/main arm64 dh-python all 6.20250414 [116 kB] Get: 51 http://deb.debian.org/debian forky/main arm64 libmarkdown2 arm64 2.2.7-2.1 [33.1 kB] Get: 52 http://deb.debian.org/debian forky/main arm64 discount arm64 2.2.7-2.1 [24.5 kB] Get: 53 http://deb.debian.org/debian forky/main arm64 dos2unix arm64 7.5.2-1+b1 [516 kB] Get: 54 http://deb.debian.org/debian forky/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 55 http://deb.debian.org/debian forky/main arm64 libcom-err2 arm64 1.47.2-3+b3 [24.9 kB] Get: 56 http://deb.debian.org/debian forky/main arm64 libnghttp3-9 arm64 1.12.0-1 [63.6 kB] Get: 57 http://deb.debian.org/debian forky/main arm64 libngtcp2-16 arm64 1.16.0-1 [123 kB] Get: 58 http://deb.debian.org/debian forky/main arm64 libidn2-0 arm64 2.3.8-4 [108 kB] Get: 59 http://deb.debian.org/debian forky/main arm64 libp11-kit0 arm64 0.25.9-2 [420 kB] Get: 60 http://deb.debian.org/debian forky/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 61 http://deb.debian.org/debian forky/main arm64 libgnutls30t64 arm64 3.8.10-2 [1395 kB] Get: 62 http://deb.debian.org/debian forky/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 63 http://deb.debian.org/debian forky/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 64 http://deb.debian.org/debian forky/main arm64 libkeyutils1 arm64 1.6.3-6 [9716 B] Get: 65 http://deb.debian.org/debian forky/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 66 http://deb.debian.org/debian forky/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 67 http://deb.debian.org/debian forky/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-10 [19.8 kB] Get: 68 http://deb.debian.org/debian forky/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-10 [55.0 kB] Get: 69 http://deb.debian.org/debian forky/main arm64 libldap2 arm64 2.6.10+dfsg-1 [179 kB] Get: 70 http://deb.debian.org/debian forky/main arm64 libnghttp2-14 arm64 1.64.0-1.1+b1 [71.7 kB] Get: 71 http://deb.debian.org/debian forky/main arm64 libngtcp2-crypto-gnutls8 arm64 1.16.0-1 [23.8 kB] Get: 72 http://deb.debian.org/debian forky/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 73 http://deb.debian.org/debian forky/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-3 [56.3 kB] Get: 74 http://deb.debian.org/debian forky/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 75 http://deb.debian.org/debian forky/main arm64 libcurl3t64-gnutls arm64 8.16.0-4 [362 kB] Get: 76 http://deb.debian.org/debian forky/main arm64 libdeflate0 arm64 1.23-2 [42.4 kB] Get: 77 http://deb.debian.org/debian forky/main arm64 libhtscodecs2 arm64 1.6.1-2 [74.7 kB] Get: 78 http://deb.debian.org/debian forky/main arm64 libhts3t64 arm64 1.22.1+ds2-1 [434 kB] Get: 79 http://deb.debian.org/debian forky/main arm64 libncurses6 arm64 6.5+20250216-2 [96.1 kB] Get: 80 http://deb.debian.org/debian forky/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 81 http://deb.debian.org/debian forky/main arm64 python3-decorator all 5.2.1-2 [33.0 kB] Get: 82 http://deb.debian.org/debian forky/main arm64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 83 http://deb.debian.org/debian forky/main arm64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 84 http://deb.debian.org/debian forky/main arm64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 85 http://deb.debian.org/debian forky/main arm64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 86 http://deb.debian.org/debian forky/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 87 http://deb.debian.org/debian forky/main arm64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 88 http://deb.debian.org/debian forky/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 89 http://deb.debian.org/debian forky/main arm64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 90 http://deb.debian.org/debian forky/main arm64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 91 http://deb.debian.org/debian forky/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 92 http://deb.debian.org/debian forky/main arm64 python3-scipy arm64 1.15.3-1.1 [15.1 MB] Get: 93 http://deb.debian.org/debian forky/main arm64 samtools arm64 1.22.1-1 [666 kB] Fetched 47.3 MB in 0s (151 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 20000 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.3-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.3-1) ... Selecting previously unselected package libpython3.13-minimal:arm64. Preparing to unpack .../libpython3.13-minimal_3.13.8-1_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.8-1) ... 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Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8 to /lib/aarch64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libhistory.so.8.2 to /lib/aarch64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8 to /lib/aarch64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/aarch64-linux-gnu/libreadline.so.8.2 to /lib/aarch64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:arm64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.8-1_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.8-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.8-1_arm64.deb ... Unpacking python3.13 (3.13.8-1) ... 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Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.193-3) ... Setting up libkrb5support0:arm64 (1.21.3-5) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg1-10) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Mon Oct 20 07:01:12 UTC 2025. Universal Time is now: Mon Oct 20 07:01:12 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libblas3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libncurses6:arm64 (6.5+20250216-2) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up python3-numpy-dev:arm64 (1:2.2.4+ds-1.2) ... Setting up autopoint (0.23.1-2) ... Setting up libk5crypto3:arm64 (1.21.3-5) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg1-10) ... Setting up libgfortran5:arm64 (15.2.0-4) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:arm64 (1.12.0-1) ... Setting up libffi8:arm64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:arm64 (0.0.8-2) ... Setting up libtasn1-6:arm64 (4.20.0-2) ... Setting up netbase (6.5) ... Setting up libngtcp2-16:arm64 (1.16.0-1) ... Setting up libkrb5-3:arm64 (1.21.3-5) ... Setting up dos2unix (7.5.2-1+b1) ... Setting up libssh2-1t64:arm64 (1.11.1-1) ... Setting up readline-common (8.3-3) ... Setting up libmarkdown2:arm64 (2.2.7-2.1) ... Setting up libldap2:arm64 (2.6.10+dfsg-1) ... 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 (1.15.0-1) ... Setting up liblapack3:arm64 (3.12.1-7) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:arm64 (2.3.8-4) ... Setting up discount (2.2.7-2.1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libp11-kit0:arm64 (0.25.9-2) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up libreadline8t64:arm64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:arm64 (3.13.8-1) ... Setting up libpython3-stdlib:arm64 (3.13.7-1) ... Setting up libgnutls30t64:arm64 (3.8.10-2) ... Setting up python3.13 (3.13.8-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up bowtie2 (2.5.4-1+b2) ... Setting up python3-decorator (5.2.1-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-3) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up python3-numpy (1:2.2.4+ds-1.2) ... Setting up libngtcp2-crypto-gnutls8:arm64 (1.16.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up python3-scipy (1.15.3-1.1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up libcurl3t64-gnutls:arm64 (8.16.0-4) ... Setting up debhelper (13.28) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up libhts3t64:arm64 (1.22.1+ds2-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up samtools (1.22.1-1) ... 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/srst2-0.2.0/ && 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 > ../srst2_0.2.0-13_source.changes dpkg-buildpackage: info: source package srst2 dpkg-buildpackage: info: source version 0.2.0-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_auto_build I: pybuild base:311: /usr/bin/python3 setup.py build markdown README.md > README.html markdown database_clustering/README.md > database_clustering_README.html make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' cd tests && python3 test_slurm_srst2.py && python3 test_srst2.py ........... ---------------------------------------------------------------------- Ran 11 tests in 0.016s OK ................. ---------------------------------------------------------------------- Ran 17 tests in 0.019s OK make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/srst2/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/srst2-0.2.0/debian/srst2 /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. !! ******************************************************************************** Please avoid running ``setup.py`` directly. Instead, use pypa/build, pypa/installer or other standards-based tools. See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. ******************************************************************************** !! self.initialize_options() debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_install mv debian/srst2/usr/lib/*/dist-packages/srst2/* debian/srst2/usr/share/srst2 rm -rf debian/*/usr/bin/*.py debian/srst2/usr/lib/*/dist-packages/ # fix line endings to make sure Python3 interpreter will be found find debian/*/usr/share -name "VFDB*" -exec dos2unix \{\} \; dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDBgenus.py to Unix format... dos2unix: converting file debian/srst2/usr/share/srst2/database_clustering/VFDB_cdhit_to_csv.py to Unix format... sed -i '1s:^#!/usr/local.*python[.0-9]*$:#!/usr/bin/python3:' debian/srst2/usr/share/srst2/qsub_srst2.py find debian -name __pycache__ -type d | xargs rm -rf make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' debian/rules override_dh_installdocs make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_installdocs sed -i "s?sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__).*scripts.*?sys.path.append(os.path.abspath('/usr/share/srst2'))?" debian/srst2/usr/share/doc/srst2/tests/*.py make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/srst2/usr/bin/srst2 dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild debian/rules override_dh_fixperms make[1]: Entering directory '/build/reproducible-path/srst2-0.2.0' dh_fixperms chmod +x debian/srst2/usr/share/srst2/database_clustering/get_genus_vfdb.sh chmod +x debian/srst2/usr/share/srst2/database_clustering/get_all_vfdb.sh chmod -x debian/srst2/usr/share/srst2/database_clustering/align_plot_tree_min3.py for py in `find debian -name "*.py"` ; do \ if head -n 1 $py | grep -q '^#! */usr/bin/.*python' ; then chmod +x $py ; fi ; \ done make[1]: Leaving directory '/build/reproducible-path/srst2-0.2.0' dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'srst2' in '../srst2_0.2.0-13_arm64.deb'. dpkg-genbuildinfo --build=binary -O../srst2_0.2.0-13_arm64.buildinfo dpkg-genchanges --build=binary -O../srst2_0.2.0-13_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/901986 and its subdirectories I: Current time: Sun Oct 19 19:01:37 -12 2025 I: pbuilder-time-stamp: 1760943697 Mon Oct 20 07:01:38 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Mon Oct 20 07:01:38 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Mon Oct 20 07:02:44 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Mon Oct 20 07:02:45 UTC 2025 I: srst2_0.2.0-13_arm64.changes: Format: 1.8 Date: Thu, 05 Dec 2024 22:13:26 +0100 Source: srst2 Binary: srst2 Architecture: arm64 Version: 0.2.0-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: srst2 - Short Read Sequence Typing for Bacterial Pathogens Closes: 1087097 Changes: srst2 (0.2.0-13) unstable; urgency=medium . * syntax-warning.patch: new: fix Python SyntaxWarning. (Closes: #1087097) * d/patches/*: normalize last update timestamp. Checksums-Sha1: 6957ef9c691d955104cda21dcafbe48cbe4ecb27 6534 srst2_0.2.0-13_arm64.buildinfo 85ba0c119f596223f600e7c1e6d9863686c957d9 61288 srst2_0.2.0-13_arm64.deb Checksums-Sha256: 10e20a6a9fa5e5f303f7c1fd65f04b4c982e670de5d2735d66abdd4dfbe04c08 6534 srst2_0.2.0-13_arm64.buildinfo bffb7ce9d08186b187ab4e0d91c7211caff611b5bcb7b08cb3825e7d27ad707b 61288 srst2_0.2.0-13_arm64.deb Files: 2a0c3d10f8e817f80a42261d411b74e5 6534 science optional srst2_0.2.0-13_arm64.buildinfo d9eea0d4fc3b3b72c0d91837be323364 61288 science optional srst2_0.2.0-13_arm64.deb Mon Oct 20 07:02:45 UTC 2025 I: diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_12-125615.service; invocation ID: 122605eb9352475286d6a6542b62bc77 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.VpKMndip/srst2_0.2.0-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.VpKMndip/srst2_0.2.0-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.VpKMndip/srst2_0.2.0-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.VpKMndip/b1/srst2_0.2.0-13_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.VpKMndip/b2/srst2_0.2.0-13_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: 207ms CPU time consumed: 174ms Memory peak: 18M (swap: 0B) Mon Oct 20 07:02:46 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Mon Oct 20 07:02:46 UTC 2025 I: srst2 from forky built successfully and reproducibly on arm64. Mon Oct 20 07:02:47 UTC 2025 I: Removing signed srst2_0.2.0-13_arm64.buildinfo.asc files: removed './b1/srst2_0.2.0-13_arm64.buildinfo.asc' removed './b2/srst2_0.2.0-13_arm64.buildinfo.asc'