Mon Jan 13 15:14:47 UTC 2025 I: starting to build porechop/experimental/amd64 on jenkins on '2025-01-13 15:14' Mon Jan 13 15:14:47 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_32/30367/console.log Mon Jan 13 15:14:47 UTC 2025 I: Downloading source for experimental/porechop=0.2.4+dfsg-8 --2025-01-13 15:14:48-- http://cdn-fastly.deb.debian.org/debian/pool/main/p/porechop/porechop_0.2.4%2bdfsg-8.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2123 (2.1K) [text/prs.lines.tag] Saving to: ‘porechop_0.2.4+dfsg-8.dsc’ 0K .. 100% 192M=0s 2025-01-13 15:14:48 (192 MB/s) - ‘porechop_0.2.4+dfsg-8.dsc’ saved [2123/2123] Mon Jan 13 15:14:48 UTC 2025 I: porechop_0.2.4+dfsg-8.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: porechop Binary: porechop Architecture: any Version: 0.2.4+dfsg-8 Maintainer: Debian Med Packaging Team Uploaders: Cédric Lood , Andreas Tille Homepage: https://rrwick.github.io/Porechop Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/porechop Vcs-Git: https://salsa.debian.org/med-team/porechop.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-sequence-python3, libseqan2-dev (= 2.5.0~rc3+dfsg-1), python3-dev, python3-setuptools Package-List: porechop deb science optional arch=any Checksums-Sha1: ca42641ad185404433d21282554185aa184bf437 726312 porechop_0.2.4+dfsg.orig.tar.xz 25eeaf244332732a7b189cbe7b16dac823083e51 7408 porechop_0.2.4+dfsg-8.debian.tar.xz Checksums-Sha256: 6d018c3c39777b36697cb1182ecaac9f981ee78c3660347fb83e52351cd79a2c 726312 porechop_0.2.4+dfsg.orig.tar.xz 49b839a70da071edfc4946ffee2560e8eb8cb8279bf5c3922e6596658d54d2db 7408 porechop_0.2.4+dfsg-8.debian.tar.xz Files: a09d363d707181eb1013200716142ad7 726312 porechop_0.2.4+dfsg.orig.tar.xz 2e3634a7a092c06c51a1a4e22c8fd641 7408 porechop_0.2.4+dfsg-8.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmdV/g0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtH8EA/+O9fhWj4x7GhTkhceZhlMYmHJXSZL8Wcu LMA5upgo6VwvQOCLnMUULy11ehGqXuumeIMURz60dlXcsB1a+i6f/3ctfI39GKl9 ISJEQzYDWpNdWr21oWZnMJyWf+ureGGYVzN2DMMib7chUvSnLzUlC0FxXiJsRcZi eXSNSHhHWkcXk2cI0IHyUIOk+eu2h3vrh4eH3zJ9T/ystKFAnZKelNjf5C9mOpk2 tlK13A6KIgjfv1z1VnH0JMfQb0divXn+nP0x7bGq/6hmFWix/HJrB3WHN94Hyhig kRP/B0VN9hgj238YpmpXPjDgrp7vU48yvs6o35F6FImosBGxA2WuutHmdU8X7RCP WquXyMrzsxL1QNHhqeT4C0+PDYung7Vfy/16XGDoxsjLKCCooQdTHkX74lEUstXa yDBWYDf/fbwTOC6dS94akLNJKLFNmJTCzdJcdwmcQPFBS3npVb7zZV8t7Jx3WmKV ZzcwnSC08Aa8Ozb0cHScCH2btCKYcn5YF08gWE1wsE0KJgfcKTwpwL2EM+yrYIXj +hN/kVm/Y94V1Usj9sTkWovSezUbLdR9wMKyAqihybuyUb6v9qwhFZ2HvFkq4kx1 wlPuDUnpkigwnF9a2TxOvsUmcG23Luhhdj5l4UxdjFxK/dU0zznr0N1cmYfaG+cb cMaKqJRLz2w= =WpoA -----END PGP SIGNATURE----- Mon Jan 13 15:14:48 UTC 2025 I: Checking whether the package is not for us Mon Jan 13 15:14:48 UTC 2025 I: Starting 1st build on remote node ionos5-amd64.debian.net. Mon Jan 13 15:14:48 UTC 2025 I: Preparing to do remote build '1' on ionos5-amd64.debian.net. Mon Jan 13 15:15:42 UTC 2025 I: Deleting $TMPDIR on ionos5-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sun Feb 15 09:37:49 -12 2026 I: pbuilder-time-stamp: 1771191469 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-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 [porechop_0.2.4+dfsg-8.dsc] I: copying [./porechop_0.2.4+dfsg.orig.tar.xz] I: copying [./porechop_0.2.4+dfsg-8.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./porechop_0.2.4+dfsg-8.dsc: unsupported subcommand dpkg-source: info: extracting porechop in porechop-0.2.4+dfsg dpkg-source: info: unpacking porechop_0.2.4+dfsg.orig.tar.xz dpkg-source: info: unpacking porechop_0.2.4+dfsg-8.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_python_interpreter_line.patch dpkg-source: info: applying no_soname.patch dpkg-source: info: applying define-all-attribute-in-clean.patch dpkg-source: info: applying 0004-Upgrade-to-SeqAn-2.5.0.patch dpkg-source: info: applying hardening dpkg-source: info: applying python3.12-syntax.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/3798160/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='experimental' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c74ac252b9664eb585371b03eab3f6c2' 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='3798160' 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.ZUO7ROjr/pbuilderrc_6QaO --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/b1 --logfile b1/build.log porechop_0.2.4+dfsg-8.dsc' SUDO_GID='110' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos5-amd64 6.11.10+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.10-1~bpo12+1 (2024-12-19) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/3798160/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: amd64 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, libseqan2-dev (= 2.5.0~rc3+dfsg-1), python3-dev, python3-setuptools dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19849 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 libseqan2-dev (= 2.5.0~rc3+dfsg-1); however: Package libseqan2-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools 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-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 37.4 MB of archives. After unpacking 147 MB will be used. The following packages have unmet dependencies: pbuilder-satisfydepends-dummy : Depends: libseqan2-dev (= 2.5.0~rc3+dfsg-1) but it is not going to be installed The following actions will resolve these dependencies: Install the following packages: 1) libseqan2-dev [2.5.0~rc3+dfsg-1 (experimental)] The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libexpat1-dev{a} libffi8{a} libfile-stripnondeterminism-perl{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} libmagic-mgc{a} libmagic1t64{a} libpipeline1{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libreadline8t64{a} libseqan2-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libxml2{a} m4{a} man-db{a} media-types{a} netbase{a} po-debconf{a} python3{a} python3-autocommand{a} python3-dev{a} python3-inflect{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-minimal{a} python3-more-itertools{a} python3-pkg-resources{a} python3-setuptools{a} python3-typeguard{a} python3-typing-extensions{a} python3-zipp{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} readline-common{a} sensible-utils{a} tzdata{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx wget 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 38.6 MB of archives. After unpacking 161 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-3 [858 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-3 [2202 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-5 [256 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-3 [1973 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-3 [740 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.1-2 [9952 B] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.1-2 [28.0 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-4 [200 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.3-1 [92.1 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-4 [723 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-2 [539 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-6 [9421 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-4 [1600 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.6.0-1 [222 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.6.0-1 [720 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250108 [113 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-4 [30.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.1-3 [2151 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.1-3 [5013 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.1-2 [10.2 kB] Get: 65 http://deb.debian.org/debian experimental/main amd64 libseqan2-dev all 2.5.0~rc3+dfsg-1 [1222 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.1-3 [507 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.1-2 [26.1 kB] Fetched 38.6 MB in 0s (133 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal:amd64. (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 ... 19849 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.1-3_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.1-3) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... 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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/porechop-0.2.4+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 > ../porechop_0.2.4+dfsg-8_source.changes dpkg-buildpackage: info: source package porechop dpkg-buildpackage: info: source version 0.2.4+dfsg-8 dpkg-buildpackage: info: source distribution experimental dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --buildsystem pybuild dh_auto_clean -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py clean running clean Deleting directory: /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build dh_autoreconf_clean -O--buildsystem=pybuild debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_clean # Removing left .so files. find . -name "*.so" -delete make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' 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 running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build running build running build_py creating /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop copying porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop Cleaning previous compilation: make clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' rm -f porechop/src/adapter_align.o porechop/src/alignment.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' Compiling Porechop: make -j 8 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/alignment.o porechop/src/alignment.cpp g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -o porechop/cpp_functions.so porechop/src/adapter_align.o porechop/src/alignment.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_auto_test -O--buildsystem=pybuild create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install --destdir=debian/porechop/ -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop running install /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66: 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() running build running build_py Cleaning previous compilation: make clean make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' rm -f porechop/src/adapter_align.o porechop/src/alignment.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' Compiling Porechop: make -j 8 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/adapter_align.o porechop/src/adapter_align.cpp g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -c -o porechop/src/alignment.o porechop/src/alignment.cpp g++ -std=c++17 -Iporechop/include -fPIC -O3 -D NDEBUG -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/reproducible-path/porechop-0.2.4+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wl,-z,relro -Wl,-z,now -shared -o porechop/cpp_functions.so porechop/src/adapter_align.o porechop/src/alignment.o make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' running install_lib creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages creating /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/porechop.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/version.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/__init__.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/nanopore_read.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/cpp_function_wrappers.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/misc.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop copying /build/reproducible-path/porechop-0.2.4+dfsg/.pybuild/cpython3_3.13/build/porechop/adapters.py -> /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/porechop.py to porechop.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/version.py to version.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/nanopore_read.py to nanopore_read.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/cpp_function_wrappers.py to cpp_function_wrappers.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/misc.py to misc.cpython-313.pyc byte-compiling /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop/adapters.py to adapters.cpython-313.pyc running install_egg_info running egg_info creating porechop.egg-info writing porechop.egg-info/PKG-INFO writing dependency_links to porechop.egg-info/dependency_links.txt writing entry points to porechop.egg-info/entry_points.txt writing top-level names to porechop.egg-info/top_level.txt writing manifest file 'porechop.egg-info/SOURCES.txt' reading manifest file 'porechop.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' adding license file 'LICENSE' writing manifest file 'porechop.egg-info/SOURCES.txt' Copying porechop.egg-info to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/lib/python3.13/dist-packages/porechop-0.2.4.egg-info Skipping SOURCES.txt running install_scripts Installing porechop script to /build/reproducible-path/porechop-0.2.4+dfsg/debian/porechop/usr/bin debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_install mv -v debian/porechop/usr/bin/porechop-runner.py debian/porechop/usr/bin/porechop renamed 'debian/porechop/usr/bin/porechop-runner.py' -> 'debian/porechop/usr/bin/porechop' make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/reproducible-path/porechop-0.2.4+dfsg' dh_python3 --no-ext-rename I: dh_python3 tools:113: replacing shebang in debian/porechop/usr/bin/porechop make[1]: Leaving directory '/build/reproducible-path/porechop-0.2.4+dfsg' 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 dh_fixperms -O--buildsystem=pybuild 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 'porechop' in '../porechop_0.2.4+dfsg-8_amd64.deb'. dpkg-deb: building package 'porechop-dbgsym' in '../porechop-dbgsym_0.2.4+dfsg-8_amd64.deb'. dpkg-genbuildinfo --build=binary -O../porechop_0.2.4+dfsg-8_amd64.buildinfo dpkg-genchanges --build=binary -O../porechop_0.2.4+dfsg-8_amd64.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/3798160 and its subdirectories I: Current time: Sun Feb 15 09:38:41 -12 2026 I: pbuilder-time-stamp: 1771191521 Mon Jan 13 15:15:42 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Mon Jan 13 15:15:42 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Mon Jan 13 15:24:04 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Mon Jan 13 15:24:05 UTC 2025 I: porechop_0.2.4+dfsg-8_amd64.changes: Format: 1.8 Date: Sun, 08 Dec 2024 21:07:46 +0100 Source: porechop Binary: porechop porechop-dbgsym Architecture: amd64 Version: 0.2.4+dfsg-8 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: porechop - adapter trimmer for Oxford Nanopore reads Closes: 1085786 Changes: porechop (0.2.4+dfsg-8) experimental; urgency=medium . * Fix Python3.12 string syntax Closes: #1085786 * Build-Depends: s/dh-python/dh-sequence-python3/ Checksums-Sha1: f16d82c13f497c89fb8a03df9ec693acabd7c105 400212 porechop-dbgsym_0.2.4+dfsg-8_amd64.deb 99723ef74fc027d76b20e62aeabcd9abe28d2ebd 6229 porechop_0.2.4+dfsg-8_amd64.buildinfo bde188b7027e3bba95c6cd7e68a184aeb6c81071 57764 porechop_0.2.4+dfsg-8_amd64.deb Checksums-Sha256: 81bd11f8030e54272b3e78503290eb93294b8c097a22b082670ab37ff2d543c2 400212 porechop-dbgsym_0.2.4+dfsg-8_amd64.deb 4c742a6722656b255e902ce9d80c5cba1dcf5f519484314bb036376c2b9d6b29 6229 porechop_0.2.4+dfsg-8_amd64.buildinfo 955465c4c472470442791d64194d1bb8d8d935d276b7feb324441ba5b7b90eed 57764 porechop_0.2.4+dfsg-8_amd64.deb Files: 362b53b46f05738cc3023467f40ed76f 400212 debug optional porechop-dbgsym_0.2.4+dfsg-8_amd64.deb a68a75099508cfeeecbe6975c176e90b 6229 science optional porechop_0.2.4+dfsg-8_amd64.buildinfo 38a96d7fe4cc75a0fe029a752576b38c 57764 science optional porechop_0.2.4+dfsg-8_amd64.deb Mon Jan 13 15:24:05 UTC 2025 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_32-30367.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/porechop_0.2.4+dfsg-8.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/porechop_0.2.4+dfsg-8.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/porechop_0.2.4+dfsg-8.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/b1/porechop_0.2.4+dfsg-8_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ZUO7ROjr/b2/porechop_0.2.4+dfsg-8_amd64.changes ## close_archive (total time: 0.000s) 0.000s 18 calls diffoscope.comparators.xz.XzContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## command (total time: 2.522s) 1.027s 55 calls diff 0.867s 77 calls objdump 0.347s 416 calls readelf 0.177s 2 calls objcopy 0.094s 18 calls xz 0.008s 11 calls strings 0.001s 19 calls cmp (internal) ## compare_files (cumulative) (total time: 12.654s) 2.301s 1 call abc.DotChangesFile 2.288s 2 calls abc.DebFile 2.253s 4 calls abc.XzFile 2.136s 2 calls abc.DebDataTarFile 2.024s 1 call abc.ElfFile 1.439s 5 calls diffoscope.comparators.elf.ElfCodeSection 0.130s 12 calls diffoscope.comparators.elf.ElfSection 0.056s 2 calls abc.TarFile 0.012s 1 call abc.TextFile 0.008s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection 0.007s 2 calls abc.Md5sumsFile ## container_extract (total time: 0.125s) 0.095s 18 calls diffoscope.comparators.xz.XzContainer 0.012s 38 calls diffoscope.comparators.deb.DebTarContainer 0.009s 22 calls diffoscope.comparators.deb.DebContainer 0.008s 20 calls diffoscope.comparators.tar.TarContainer ## diff (total time: 0.774s) 0.774s 356 calls linediff ## has_same_content_as (total time: 0.002s) 0.001s 6 calls abc.TextFile 0.000s 4 calls abc.Md5sumsFile 0.000s 4 calls abc.XzFile 0.000s 2 calls abc.DebDataTarFile 0.000s 2 calls abc.TarFile 0.000s 2 calls abc.DebFile 0.000s 1 call abc.ElfFile 0.000s 1 call abc.DotChangesFile 0.000s 1 call diffoscope.comparators.utils.libarchive.LibarchiveSymlink 0.000s 12 calls diffoscope.comparators.elf.ElfSection 0.000s 5 calls diffoscope.comparators.elf.ElfCodeSection 0.000s 1 call diffoscope.comparators.elf.MonkeyPatchedElfSection ## main (total time: 10.095s) 10.094s 2 calls outputs 0.000s 1 call cleanup ## open_archive (total time: 0.000s) 0.000s 18 calls diffoscope.comparators.xz.XzContainer 0.000s 12 calls diffoscope.comparators.tar.TarContainer 0.000s 8 calls diffoscope.comparators.deb.DebContainer 0.000s 6 calls diffoscope.comparators.deb.DebTarContainer ## output (total time: 7.472s) 7.414s 1 call html 0.033s 1 call text 0.025s 1 call json ## recognizes (total time: 0.156s) 0.071s 1674 calls diffoscope.comparators.utils.libarchive.LibarchiveMember 0.059s 780 calls diffoscope.comparators.utils.archive.ArchiveMember 0.018s 12 calls diffoscope.comparators.binary.FilesystemFile 0.008s 216 calls diffoscope.comparators.debian.DebControlMember ## specialize (total time: 0.052s) 0.052s 41 calls specialize Finished with result: success Main processes terminated with: code=exited/status=1 Service runtime: 10.402s CPU time consumed: 10.869s Mon Jan 13 15:24:16 UTC 2025 W: Diffoscope claims the build is reproducible, but there is a diffoscope file. Please investigate. Mon Jan 13 15:24:16 UTC 2025 E: porechop failed to build reproducibly in experimental on amd64. Mon Jan 13 15:24:18 UTC 2025 I: Submitting .buildinfo files to external archives: Mon Jan 13 15:24:18 UTC 2025 I: Submitting 8.0K b1/porechop_0.2.4+dfsg-8_amd64.buildinfo.asc Mon Jan 13 15:24:20 UTC 2025 I: Submitting 8.0K b2/porechop_0.2.4+dfsg-8_amd64.buildinfo.asc Mon Jan 13 15:24:20 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Jan 13 15:24:20 UTC 2025 I: Done submitting .buildinfo files. Mon Jan 13 15:24:20 UTC 2025 I: Removing signed porechop_0.2.4+dfsg-8_amd64.buildinfo.asc files: removed './b1/porechop_0.2.4+dfsg-8_amd64.buildinfo.asc' removed './b2/porechop_0.2.4+dfsg-8_amd64.buildinfo.asc'