Running as unit: rb-build-arm64_12-92638.service ==================================================================================== Sat Apr 26 18:57:55 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_arm64_12) on jenkins, called using "codethink04-arm64 codethink03-arm64" as arguments. Sat Apr 26 18:57:55 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Ma2ICo3c" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Apr 26 18:57:55 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Apr 26 18:57:55 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-bFmYI0' Sat Apr 26 18:57:56 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Apr 26 18:57:56 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-KX3rou' ok, let's check if ragout is building anywhere yet… ok, ragout is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of ragout in unstable on arm64 on jenkins now. 1st build will be done on codethink04-arm64.debian.net. 2nd build will be done on codethink03-arm64.debian.net. ============================================================================= Sat Apr 26 18:58:11 UTC 2025 I: starting to build ragout/unstable/arm64 on jenkins on '2025-04-26 18:57' Sat Apr 26 18:58:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_12/92638/console.log 1745693891 arm64 unstable ragout Sat Apr 26 18:58:11 UTC 2025 I: Downloading source for unstable/ragout=2.3-5 --2025-04-26 18:58:11-- http://deb.debian.org/debian/pool/main/r/ragout/ragout_2.3-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2117 (2.1K) [text/prs.lines.tag] Saving to: ‘ragout_2.3-5.dsc’ 0K .. 100% 302M=0s 2025-04-26 18:58:11 (302 MB/s) - ‘ragout_2.3-5.dsc’ saved [2117/2117] --2025-04-26 18:58:11-- http://deb.debian.org/debian/pool/main/r/ragout/ragout_2.3-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2117 (2.1K) [text/prs.lines.tag] Saving to: ‘ragout_2.3-5.dsc’ 0K .. 100% 302M=0s 2025-04-26 18:58:11 (302 MB/s) - ‘ragout_2.3-5.dsc’ saved [2117/2117] Sat Apr 26 18:58:11 UTC 2025 I: ragout_2.3-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ragout Binary: ragout, ragout-examples Architecture: any all Version: 2.3-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/fenderglass/Ragout/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/ragout Vcs-Git: https://salsa.debian.org/med-team/ragout.git Testsuite: autopkgtest Testsuite-Triggers: sibelia Build-Depends: debhelper-compat (= 13), dh-sequence-python3, python3-dev, python3-networkx, python3-setuptools, python3-six Package-List: ragout deb science optional arch=any ragout-examples deb science optional arch=all Checksums-Sha1: 84bd0042b8e6241c57e2d86e31ff3c8bd2e83dae 12259072 ragout_2.3.orig.tar.xz 0b6731e88f0a726a9e59d5c8889cb08013338ac8 14976 ragout_2.3-5.debian.tar.xz Checksums-Sha256: 135d2dead97f0488b37d1ce399e84753390f61d24f7ea9513d228c802a678a1b 12259072 ragout_2.3.orig.tar.xz 17e84d4a2a9fafa5fde026380f07de6dd5405df63992b175da5c9aa5ce15b1e9 14976 ragout_2.3-5.debian.tar.xz Files: 32067eee402ee675a30f43bb14fe6cf7 12259072 ragout_2.3.orig.tar.xz 6af58bef1f9a56718e3e7e824c6ab355 14976 ragout_2.3-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmW8wNMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtG+Ew/9GHkNHq1Yb7svTOeIlls3swsQd5T8IvjZ Kwzj+6heTVxWGTz4ILlcWi2stpwOrWgBlH9KPKz+s1vaG6x/uCFUhfqlYLY/KiU7 DmGq9MCZ2puvGL+OaMBTE0UGOT99pQKMIIAKY4FdbxDXUFhrLDYjNzvyvIud5GX9 h8/xekBdYsznupxUrBNE6n6gGOaSqzAjKRe1g1oqR5vj67KgwEjqoozZWxUZewjE O+YWU1mQWZfqAmUxF0AiBlsSMz4E8LItbew0o2g8Egp0azroYmXgeWLReLFQSaUJ oWBzC30oDy9b08VPVLW1vm2DMdw4beK9KcKb47hXSdVznvODMOH1xQu+ABKT2FZW 9aHZKqNOfPPohzc84UaruhWvAhdMoHhleFIDtiInvh6Z/iJ5WtbH2YT0yN8xPkyZ ZlGi1emSPAGePhBjGr34TbFD+bjwgv6pk7r+igNT0oPg/GK32++j9H8+G9uQvqy2 T0LNyPIYrm32UPUWKPZdJB3jY/KxbgoR4+nZxtDT4of5MEVdeVRawo6wa6xhKI75 sn4UdldOxeTixWEER6Awa9tbEkmGPI8Idta1vvG6kV63NEfKtLJAq4292s4kPWX5 8J+WnniEe3ftEdokoQ6VLZfmsJkDqjVk3d000ivX09tZLzRhKyCr6YXz7o465rwY BnD18zAt7Ro= =4WoB -----END PGP SIGNATURE----- Sat Apr 26 18:58:11 UTC 2025 I: Checking whether the package is not for us Sat Apr 26 18:58:11 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Sat Apr 26 18:58:11 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Sat Apr 26 18:58:11 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink04-arm64.debian.net is marked as down. Sat Apr 26 18:58:11 UTC 2025 - checking via ssh if codethink04-arm64.debian.net is up. removed '/tmp/read-only-fs-test-UrKInc' ==================================================================================== Sat Apr 26 18:58:13 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink04-arm64, called using "1 ragout unstable /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5 2.3-5" as arguments. Sat Apr 26 18:58:13 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-AN6iHPLd" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat Apr 26 18:58:13 UTC 2025 I: Downloading source for unstable/ragout=2.3-5 Reading package lists... NOTICE: 'ragout' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ragout.git Please use: git clone https://salsa.debian.org/med-team/ragout.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 12.3 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main ragout 2.3-5 (dsc) [2117 B] Get:2 http://deb.debian.org/debian unstable/main ragout 2.3-5 (tar) [12.3 MB] Get:3 http://deb.debian.org/debian unstable/main ragout 2.3-5 (diff) [15.0 kB] Fetched 12.3 MB in 0s (41.4 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'ragout' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ragout.git Please use: git clone https://salsa.debian.org/med-team/ragout.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 12.3 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main ragout 2.3-5 (dsc) [2117 B] Get:2 http://deb.debian.org/debian unstable/main ragout 2.3-5 (tar) [12.3 MB] Get:3 http://deb.debian.org/debian unstable/main ragout 2.3-5 (diff) [15.0 kB] Fetched 12.3 MB in 0s (41.4 MB/s) Download complete and in download only mode ============================================================================= Building ragout in unstable on arm64 on codethink04-arm64 now. Date: Sat Apr 26 19:58:13 BST 2025 Date UTC: Sat Apr 26 18:58:13 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 26 06:58:14 -12 2025 I: pbuilder-time-stamp: 1745693894 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ragout_2.3-5.dsc] I: copying [./ragout_2.3.orig.tar.xz] I: copying [./ragout_2.3-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: unsupported subcommand dpkg-source: info: extracting ragout in ragout-2.3 dpkg-source: info: unpacking ragout_2.3.orig.tar.xz dpkg-source: info: unpacking ragout_2.3-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying connected_component_subgraphs.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/463253/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='da9751a376d8408986101ddf96d27f74' 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='463253' 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.AqJWWNr5/pbuilderrc_QvjU --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1 --logfile b1/build.log ragout_2.3-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/463253/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-dev, python3-networkx, python3-setuptools, python3-six dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six 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} 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-networkx{a} python3-pkg-resources{a} python3-setuptools{a} python3-six{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 python3-gdal python3-matplotlib python3-numpy python3-pydot python3-pygraphviz python3-scipy python3-yaml wget 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 40.2 MB of archives. After unpacking 194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.1-1 [145 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.3-2 [1975 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.3-2 [4688 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.3-1 [10.4 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.3-2 [508 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.3-1 [26.1 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.0-1.2 [224 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.0-1.2 [738 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] Fetched 40.2 MB in 0s (201 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19953 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... 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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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 26 18:58:32 UTC 2025. Universal Time is now: Sat Apr 26 18:58:32 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.1-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libpython3.13:arm64 (3.13.3-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:arm64 (3.13.3-2) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libpython3-dev:arm64 (3.13.3-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.3-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.3-1) ... Setting up python3-pkg-resources (78.1.0-1.2) ... Setting up python3-setuptools (78.1.0-1.2) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-7) ... 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/ragout-2.3/ && 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 > ../ragout_2.3-5_source.changes dpkg-buildpackage: info: source package ragout dpkg-buildpackage: info: source version 2.3-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_auto_clean || true I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -f bin/ragout-maf2synteny bin/ragout-overlap rm -rf .pybuild find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' 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 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/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/main.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__version__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG build_graph.cpp -o build_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG fasta.cpp -o fasta.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG overlap.cpp -o overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG suffix_array.cpp -o suffix_array.o g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG breakpoint_graph.cpp -o breakpoint_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG compress_algorithms.cpp -o compress_algorithms.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG maf_tools.cpp -o maf_tools.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG permutation.cpp -o permutation.o g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/ragout-2.3/debian/tmp running install /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() running build running build_py /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' running install_lib creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/test_toy.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__version__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/main.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/test_toy.py to test_toy.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/lexer.py to lexer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tokens.py to tokens.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tree.py to tree.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/cactus.py to cactus.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/hal.py to hal.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/maf.py to maf.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/sibelia.py to sibelia.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/synteny_backend.py to synteny_backend.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/config.py to config.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/debug.py to debug.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/utils.py to utils.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/datatypes.py to datatypes.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/merge_iters.py to merge_iters.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/output_generator.py to output_generator.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/scaffolder.py to scaffolder.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/phylogeny.py to phylogeny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/phylogeny_parser.py to phylogeny_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/fasta_parser.py to fasta_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/recipe_parser.py to recipe_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/overlap.py to overlap.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/maf2synteny.py to maf2synteny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/breakpoint_graph.py to breakpoint_graph.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/chimera_detector.py to chimera_detector.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/permutation.py to permutation.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/repeat_resolver.py to repeat_resolver.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/assembly_refine.py to assembly_refine.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__version__.py to __version__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/main.py to main.cpython-313.pyc running install_egg_info running egg_info creating ragout.egg-info writing ragout.egg-info/PKG-INFO writing dependency_links to ragout.egg-info/dependency_links.txt writing entry points to ragout.egg-info/entry_points.txt writing top-level names to ragout.egg-info/top_level.txt writing manifest file 'ragout.egg-info/SOURCES.txt' reading manifest file 'ragout.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'ragout.egg-info/SOURCES.txt' Copying ragout.egg-info to /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout-2.3.egg-info Skipping SOURCES.txt running install_scripts Installing ragout script to /build/reproducible-path/ragout-2.3/debian/tmp/usr/bin Installing C++ binaries debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_install find debian -name LICENSE -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/ragout/usr/bin/ragout 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${python3:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ragout' in '../ragout_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_arm64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_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/463253 and its subdirectories I: Current time: Sat Apr 26 07:00:21 -12 2025 I: pbuilder-time-stamp: 1745694021 Sat Apr 26 19:00:21 UTC 2025 I: Signing ./b1/ragout_2.3-5_arm64.buildinfo as ragout_2.3-5_arm64.buildinfo.asc Sat Apr 26 19:00:21 UTC 2025 I: Signed ./b1/ragout_2.3-5_arm64.buildinfo as ./b1/ragout_2.3-5_arm64.buildinfo.asc Sat Apr 26 19:00:21 UTC 2025 - build #1 for ragout/unstable/arm64 on codethink04-arm64 done. Starting cleanup. All cleanup done. Sat Apr 26 19:00:21 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-AN6iHPLd, removing. /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Apr 26 19:00 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 26 18:58 b2 -rw-r--r-- 1 jenkins jenkins 2117 Feb 2 2024 ragout_2.3-5.dsc -rw------- 1 jenkins jenkins 3210 Apr 26 18:58 rbuildlog.83wM4kB /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1: total 21464 -rw-r--r-- 1 jenkins jenkins 70716 Apr 26 19:00 build.log -rw-r--r-- 1 jenkins jenkins 1304292 Apr 26 19:00 ragout-dbgsym_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Apr 26 19:00 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Apr 26 19:00 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Apr 26 19:00 ragout_2.3-5.dsc -rw-r--r-- 1 jenkins jenkins 6322 Apr 26 19:00 ragout_2.3-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7204 Apr 26 19:00 ragout_2.3-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1826 Apr 26 19:00 ragout_2.3-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 2113576 Apr 26 19:00 ragout_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1315 Apr 26 19:00 ragout_2.3-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2: total 0 Sat Apr 26 19:00:22 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Apr 26 06:58:14 -12 2025 I: pbuilder-time-stamp: 1745693894 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ragout_2.3-5.dsc] I: copying [./ragout_2.3.orig.tar.xz] I: copying [./ragout_2.3-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: unsupported subcommand dpkg-source: info: extracting ragout in ragout-2.3 dpkg-source: info: unpacking ragout_2.3.orig.tar.xz dpkg-source: info: unpacking ragout_2.3-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying connected_component_subgraphs.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/463253/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='da9751a376d8408986101ddf96d27f74' 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='463253' 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.AqJWWNr5/pbuilderrc_QvjU --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1 --logfile b1/build.log ragout_2.3-5.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/463253/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-dev, python3-networkx, python3-setuptools, python3-six dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six 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} 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-networkx{a} python3-pkg-resources{a} python3-setuptools{a} python3-six{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 python3-gdal python3-matplotlib python3-numpy python3-pydot python3-pygraphviz python3-scipy python3-yaml wget 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 40.2 MB of archives. After unpacking 194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.1-1 [145 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.3-2 [1975 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.3-2 [4688 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.3-1 [10.4 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.3-2 [508 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.3-1 [26.1 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.0-1.2 [224 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.0-1.2 [738 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] Fetched 40.2 MB in 0s (201 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19953 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20287 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... 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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../9-libpython3-stdlib_3.13.3-1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.13.3-1) ... Setting up python3-minimal (3.13.3-1) ... Selecting previously unselected package python3. (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 ... 21299 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.3-1_arm64.deb ... Unpacking python3 (3.13.3-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_arm64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Apr 26 18:58:32 UTC 2025. Universal Time is now: Sat Apr 26 18:58:32 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.1-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libpython3.13:arm64 (3.13.3-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:arm64 (3.13.3-2) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libpython3-dev:arm64 (3.13.3-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.3-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.3-1) ... Setting up python3-pkg-resources (78.1.0-1.2) ... Setting up python3-setuptools (78.1.0-1.2) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-7) ... 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/ragout-2.3/ && 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 > ../ragout_2.3-5_source.changes dpkg-buildpackage: info: source package ragout dpkg-buildpackage: info: source version 2.3-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_auto_clean || true I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -f bin/ragout-maf2synteny bin/ragout-overlap rm -rf .pybuild find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' 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 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/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/main.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__version__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG build_graph.cpp -o build_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG fasta.cpp -o fasta.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG overlap.cpp -o overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG suffix_array.cpp -o suffix_array.o g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG breakpoint_graph.cpp -o breakpoint_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG compress_algorithms.cpp -o compress_algorithms.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG maf_tools.cpp -o maf_tools.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG permutation.cpp -o permutation.o g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/ragout-2.3/debian/tmp running install /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() running build running build_py /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' running install_lib creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/test_toy.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__version__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/main.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/test_toy.py to test_toy.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/lexer.py to lexer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tokens.py to tokens.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tree.py to tree.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/cactus.py to cactus.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/hal.py to hal.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/maf.py to maf.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/sibelia.py to sibelia.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/synteny_backend.py to synteny_backend.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/config.py to config.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/debug.py to debug.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/utils.py to utils.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/datatypes.py to datatypes.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/merge_iters.py to merge_iters.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/output_generator.py to output_generator.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/scaffolder.py to scaffolder.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/phylogeny.py to phylogeny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/phylogeny_parser.py to phylogeny_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/fasta_parser.py to fasta_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/recipe_parser.py to recipe_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/overlap.py to overlap.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/maf2synteny.py to maf2synteny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/breakpoint_graph.py to breakpoint_graph.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/chimera_detector.py to chimera_detector.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/permutation.py to permutation.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/repeat_resolver.py to repeat_resolver.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/assembly_refine.py to assembly_refine.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__version__.py to __version__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/main.py to main.cpython-313.pyc running install_egg_info running egg_info creating ragout.egg-info writing ragout.egg-info/PKG-INFO writing dependency_links to ragout.egg-info/dependency_links.txt writing entry points to ragout.egg-info/entry_points.txt writing top-level names to ragout.egg-info/top_level.txt writing manifest file 'ragout.egg-info/SOURCES.txt' reading manifest file 'ragout.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'ragout.egg-info/SOURCES.txt' Copying ragout.egg-info to /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout-2.3.egg-info Skipping SOURCES.txt running install_scripts Installing ragout script to /build/reproducible-path/ragout-2.3/debian/tmp/usr/bin Installing C++ binaries debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_install find debian -name LICENSE -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/ragout/usr/bin/ragout 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${python3:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ragout' in '../ragout_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_arm64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_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/463253 and its subdirectories I: Current time: Sat Apr 26 07:00:21 -12 2025 I: pbuilder-time-stamp: 1745694021 Sat Apr 26 19:00:23 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Sat Apr 26 19:00:23 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Sat Apr 26 19:00:23 UTC 2025 - checking /var/lib/jenkins/offline_nodes if codethink03-arm64.debian.net is marked as down. Sat Apr 26 19:00:23 UTC 2025 - checking via ssh if codethink03-arm64.debian.net is up. removed '/tmp/read-only-fs-test-sJ0I8u' ==================================================================================== Sat May 30 01:23:24 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on codethink03-arm64, called using "2 ragout unstable /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5 2.3-5" as arguments. Sat May 30 01:23:24 UTC 2026 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-Nop2YjhR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Sat May 30 01:23:24 UTC 2026 I: Downloading source for unstable/ragout=2.3-5 Reading package lists... NOTICE: 'ragout' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ragout.git Please use: git clone https://salsa.debian.org/med-team/ragout.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 12.3 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main ragout 2.3-5 (dsc) [2117 B] Get:2 http://deb.debian.org/debian unstable/main ragout 2.3-5 (tar) [12.3 MB] Get:3 http://deb.debian.org/debian unstable/main ragout 2.3-5 (diff) [15.0 kB] Fetched 12.3 MB in 0s (101 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'ragout' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ragout.git Please use: git clone https://salsa.debian.org/med-team/ragout.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 12.3 MB of source archives. Get:1 http://deb.debian.org/debian unstable/main ragout 2.3-5 (dsc) [2117 B] Get:2 http://deb.debian.org/debian unstable/main ragout 2.3-5 (tar) [12.3 MB] Get:3 http://deb.debian.org/debian unstable/main ragout 2.3-5 (diff) [15.0 kB] Fetched 12.3 MB in 0s (101 MB/s) Download complete and in download only mode ============================================================================= Re-Building ragout in unstable on arm64 on codethink03-arm64 now. Date: Sat May 30 02:23:25 BST 2026 Date UTC: Sat May 30 01:23:25 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5 + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/pbuilderrc_sMxr + case ${ARCH} in + case $ARCH in + locale=nl_BE + language=nl + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' ragout = debian-installer -o ragout = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' ragout = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/pbuilderrc_sMxr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2 --logfile b2/build.log ragout_2.3-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat May 30 15:23:25 +14 2026 I: pbuilder-time-stamp: 1780104205 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [ragout_2.3-5.dsc] I: copying [./ragout_2.3.orig.tar.xz] I: copying [./ragout_2.3-5.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./ragout_2.3-5.dsc: unsupported subcommand dpkg-source: info: extracting ragout in ragout-2.3 dpkg-source: info: unpacking ragout_2.3.orig.tar.xz dpkg-source: info: unpacking ragout_2.3-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying connected_component_subgraphs.patch dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D01_modify_environment starting debug: Running on codethink03-arm64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 May 30 01:23 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") BASH_VERSION='5.2.37(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' INVOCATION_ID=8f9b85855ef841f2892c3dc5d72cb9e9 LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=2956341 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/pbuilderrc_sMxr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2 --logfile b2/build.log ragout_2.3-5.dsc' SUDO_GID=109 SUDO_UID=104 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://192.168.101.4:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2956341/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-dev, python3-networkx, python3-setuptools, python3-six dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19953 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-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-networkx; however: Package python3-networkx is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-six; however: Package python3-six 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} 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-networkx{a} python3-pkg-resources{a} python3-setuptools{a} python3-six{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 python3-gdal python3-matplotlib python3-numpy python3-pydot python3-pygraphviz python3-scipy python3-yaml wget 0 packages upgraded, 67 newly installed, 0 to remove and 0 not upgraded. Need to get 40.2 MB of archives. After unpacking 194 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libpython3.13-minimal arm64 3.13.3-2 [855 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.1-1 [93.3 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 python3.13-minimal arm64 3.13.3-2 [1998 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 python3-minimal arm64 3.13.3-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 tzdata all 2025b-2 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.8-2 [21.3 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 readline-common all 8.2-6 [69.4 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-6 [159 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpython3.13-stdlib arm64 3.13.3-2 [1890 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 python3.13 arm64 3.13.3-2 [751 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 libpython3-stdlib arm64 3.13.3-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 python3 arm64 3.13.3-1 [28.2 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.25 [25.0 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.41-4 [93.9 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-8 [285 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.2 [90.9 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 36 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.4 [629 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.2 [919 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libexpat1-dev arm64 2.7.1-1 [145 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 libpython3.13 arm64 3.13.3-2 [1975 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libpython3.13-dev arm64 3.13.3-2 [4688 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 libpython3-dev arm64 3.13.3-1 [10.4 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 python3.13-dev arm64 3.13.3-2 [508 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 python3-dev arm64 3.13.3-1 [26.1 kB] Get: 56 http://deb.debian.org/debian unstable/main arm64 python3-more-itertools all 10.7.0-1 [67.4 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 python3-typing-extensions all 4.13.2-1 [90.5 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 python3-typeguard all 4.4.2-1 [37.3 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 python3-pkg-resources all 78.1.0-1.2 [224 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 64 http://deb.debian.org/debian unstable/main arm64 python3-setuptools all 78.1.0-1.2 [738 kB] Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] Fetched 40.2 MB in 0s (136 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19953 files and directories currently installed.) Preparing to unpack .../libpython3.13-minimal_3.13.3-2_arm64.deb ... Unpacking libpython3.13-minimal:arm64 (3.13.3-2) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.7.1-1_arm64.deb ... Unpacking libexpat1:arm64 (2.7.1-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.3-2_arm64.deb ... Unpacking python3.13-minimal (3.13.3-2) ... Setting up libpython3.13-minimal:arm64 (3.13.3-2) ... Setting up libexpat1:arm64 (2.7.1-1) ... Setting up python3.13-minimal (3.13.3-2) ... Selecting previously unselected package python3-minimal. (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 ... 20287 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.3-1_arm64.deb ... Unpacking python3-minimal (3.13.3-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_13.0.0_all.deb ... Unpacking media-types (13.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.5_all.deb ... Unpacking netbase (6.5) ... Selecting previously unselected package tzdata. Preparing to unpack .../3-tzdata_2025b-2_all.deb ... Unpacking tzdata (2025b-2) ... Selecting previously unselected package libffi8:arm64. Preparing to unpack .../4-libffi8_3.4.8-2_arm64.deb ... Unpacking libffi8:arm64 (3.4.8-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:arm64. Preparing to unpack .../6-libreadline8t64_8.2-6_arm64.deb ... 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 (8.2-6) ... Selecting previously unselected package libpython3.13-stdlib:arm64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.3-2_arm64.deb ... Unpacking libpython3.13-stdlib:arm64 (3.13.3-2) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.3-2_arm64.deb ... Unpacking python3.13 (3.13.3-2) ... 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Unpacking libpython3.13-dev:arm64 (3.13.3-2) ... Selecting previously unselected package libpython3-dev:arm64. Preparing to unpack .../38-libpython3-dev_3.13.3-1_arm64.deb ... Unpacking libpython3-dev:arm64 (3.13.3-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../39-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3.13-dev. Preparing to unpack .../40-python3.13-dev_3.13.3-2_arm64.deb ... Unpacking python3.13-dev (3.13.3-2) ... Selecting previously unselected package python3-dev. Preparing to unpack .../41-python3-dev_3.13.3-1_arm64.deb ... Unpacking python3-dev (3.13.3-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../42-python3-more-itertools_10.7.0-1_all.deb ... Unpacking python3-more-itertools (10.7.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../43-python3-typing-extensions_4.13.2-1_all.deb ... Unpacking python3-typing-extensions (4.13.2-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../44-python3-typeguard_4.4.2-1_all.deb ... Unpacking python3-typeguard (4.4.2-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../45-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../46-python3-jaraco.functools_4.1.0-1_all.deb ... Unpacking python3-jaraco.functools (4.1.0-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../47-python3-pkg-resources_78.1.0-1.2_all.deb ... Unpacking python3-pkg-resources (78.1.0-1.2) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../48-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:arm64 (1:5.46-5) ... Setting up gettext-base (0.23.1-1) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:arm64 (0.192-4) ... Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' Local time is now: Sat May 30 01:23:44 UTC 2026. Universal Time is now: Sat May 30 01:23:44 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:arm64 (2.7.1-1) ... Setting up libunistring5:arm64 (1.3-2) ... Setting up autopoint (0.23.1-1) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:arm64 (3.4.8-2) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:arm64 (0.0.8-1+b2) ... Setting up netbase (6.5) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:arm64 (2.12.7+dfsg+really2.9.14-0.4) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up libreadline8t64:arm64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libpython3.13-stdlib:arm64 (3.13.3-2) ... Setting up libpython3-stdlib:arm64 (3.13.3-1) ... Setting up libpython3.13:arm64 (3.13.3-2) ... Setting up python3.13 (3.13.3-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.3-1) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:arm64 (3.13.3-2) ... Setting up python3-typing-extensions (4.13.2-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.7.0-1) ... Setting up libpython3-dev:arm64 (3.13.3-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.3-2) ... Setting up python3-typeguard (4.4.2-1) ... Setting up debhelper (13.24.2) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.3-1) ... Setting up python3-pkg-resources (78.1.0-1.2) ... Setting up python3-setuptools (78.1.0-1.2) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-7) ... 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: user script /srv/workspace/pbuilder/2956341/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/ragout-2.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ragout_2.3-5_source.changes dpkg-buildpackage: info: source package ragout dpkg-buildpackage: info: source version 2.3-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_auto_clean || true I: pybuild base:311: python3.13 setup.py clean running clean removing '/build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-aarch64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -f bin/ragout-maf2synteny bin/ragout-overlap rm -rf .pybuild find . -name "*.o" -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' 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 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/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/main.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__version__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout copying ragout/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph copying ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph copying ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny copying ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap copying ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers copying ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny copying ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder copying ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared copying ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend copying ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick copying ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests copying ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests creating /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data copying ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG build_graph.cpp -o build_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG fasta.cpp -o fasta.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG overlap.cpp -o overlap.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG suffix_array.cpp -o suffix_array.o g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG breakpoint_graph.cpp -o breakpoint_graph.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG compress_algorithms.cpp -o compress_algorithms.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG maf_tools.cpp -o maf_tools.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG main.cpp -o main.o g++ -c -g -O2 -ffile-prefix-map=/build/reproducible-path/ragout-2.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -std=c++0x -Wall -O2 -DNDEBUG permutation.cpp -o permutation.o g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build; python3.13 -m unittest discover -v ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py install --root /build/reproducible-path/ragout-2.3/debian/tmp running install /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() running build running build_py /build/reproducible-path/ragout-2.3/setup.py:35: DeprecationWarning: Use shutil.which instead of find_executable if not find_executable("make"): make[1]: Entering directory '/build/reproducible-path/ragout-2.3' make -C ragout/overlap/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now build_graph.o fasta.o main.o overlap.o suffix_array.o -o /build/reproducible-path/ragout-2.3/bin/ragout-overlap make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/overlap/cpp_impl' make -C ragout/maf2synteny/cpp_impl all make[2]: Entering directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' g++ -Wl,-z,relro -Wl,-z,now breakpoint_graph.o compress_algorithms.o maf_tools.o main.o permutation.o -o /build/reproducible-path/ragout-2.3/bin/ragout-maf2synteny make[2]: Leaving directory '/build/reproducible-path/ragout-2.3/ragout/maf2synteny/cpp_impl' make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' running install_lib creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/test_toy.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__pycache__ creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/DH1.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/ecoli.rcp -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655.coords -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/data/mg1655_contigs.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/tests/test_toy.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/lexer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tokens.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/newick/tree.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/cactus.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/hal.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/maf.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/sibelia.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/synteny_backend/synteny_backend.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/config.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/debug.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/utils.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/shared/datatypes.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/merge_iters.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/output_generator.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/scaffolder/scaffolder.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/phylogeny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/phylogeny/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/phylogeny_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/fasta_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/parsers/recipe_parser.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/overlap/overlap.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/maf2synteny/maf2synteny.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/inferer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/breakpoint_graph.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/chimera_detector.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/permutation.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/breakpoint_graph/repeat_resolver.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph creating /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__pycache__/__init__.cpython-313.pyc -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__pycache__ copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/assembly_graph/assembly_refine.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/__version__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout copying /build/reproducible-path/ragout-2.3/.pybuild/cpython3_3.13/build/ragout/main.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/test_toy.py to test_toy.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/lexer.py to lexer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/parser.py to parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tokens.py to tokens.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick/tree.py to tree.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/cactus.py to cactus.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/hal.py to hal.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/maf.py to maf.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/sibelia.py to sibelia.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/synteny_backend/synteny_backend.py to synteny_backend.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/config.py to config.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/debug.py to debug.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/utils.py to utils.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/shared/datatypes.py to datatypes.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/merge_iters.py to merge_iters.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/output_generator.py to output_generator.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/scaffolder/scaffolder.py to scaffolder.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/phylogeny.py to phylogeny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/phylogeny/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/phylogeny_parser.py to phylogeny_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/fasta_parser.py to fasta_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/parsers/recipe_parser.py to recipe_parser.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/overlap/overlap.py to overlap.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/maf2synteny/maf2synteny.py to maf2synteny.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/inferer.py to inferer.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/breakpoint_graph.py to breakpoint_graph.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/chimera_detector.py to chimera_detector.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/permutation.py to permutation.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/breakpoint_graph/repeat_resolver.py to repeat_resolver.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph/assembly_refine.py to assembly_refine.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__init__.py to __init__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/__version__.py to __version__.cpython-313.pyc byte-compiling /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/main.py to main.cpython-313.pyc running install_egg_info running egg_info creating ragout.egg-info writing ragout.egg-info/PKG-INFO writing dependency_links to ragout.egg-info/dependency_links.txt writing entry points to ragout.egg-info/entry_points.txt writing top-level names to ragout.egg-info/top_level.txt writing manifest file 'ragout.egg-info/SOURCES.txt' reading manifest file 'ragout.egg-info/SOURCES.txt' adding license file 'LICENSE' writing manifest file 'ragout.egg-info/SOURCES.txt' Copying ragout.egg-info to /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout-2.3.egg-info Skipping SOURCES.txt running install_scripts Installing ragout script to /build/reproducible-path/ragout-2.3/debian/tmp/usr/bin Installing C++ binaries debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/ragout-2.3' dh_install find debian -name LICENSE -delete make[1]: Leaving directory '/build/reproducible-path/ragout-2.3' dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild dh_installman -O--buildsystem=pybuild dh_python3 -O--buildsystem=pybuild I: dh_python3 tools:114: replacing shebang in debian/ragout/usr/bin/ragout 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 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package ragout-examples: substitution variable ${python3:Depends} used, but is not defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ragout' in '../ragout_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_arm64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_arm64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_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: user script /srv/workspace/pbuilder/2956341/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/B01_cleanup finished 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/2956341 and its subdirectories I: Current time: Sat May 30 15:25:39 +14 2026 I: pbuilder-time-stamp: 1780104339 + false + set +x Sat May 30 01:25:39 UTC 2026 I: Signing ./b2/ragout_2.3-5_arm64.buildinfo as ragout_2.3-5_arm64.buildinfo.asc Sat May 30 01:25:39 UTC 2026 I: Signed ./b2/ragout_2.3-5_arm64.buildinfo as ./b2/ragout_2.3-5_arm64.buildinfo.asc Sat May 30 01:25:39 UTC 2026 - build #2 for ragout/unstable/arm64 on codethink03-arm64 done. Starting cleanup. All cleanup done. Sat May 30 01:25:39 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Nop2YjhR, removing. /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5: total 92 drwxr-xr-x 2 jenkins jenkins 4096 Apr 26 19:00 b1 drwxr-xr-x 2 jenkins jenkins 4096 Apr 26 19:02 b2 -rw-r--r-- 1 jenkins jenkins 2117 Feb 2 2024 ragout_2.3-5.dsc -rw------- 1 jenkins jenkins 74227 Apr 26 19:00 rbuildlog.83wM4kB /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1: total 21500 -rw-r--r-- 1 jenkins jenkins 70716 Apr 26 19:00 build.log -rw-r--r-- 1 jenkins jenkins 1304292 Apr 26 19:00 ragout-dbgsym_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Apr 26 19:00 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Apr 26 19:00 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Apr 26 19:00 ragout_2.3-5.dsc -rw-r--r-- 1 jenkins jenkins 6322 Apr 26 19:00 ragout_2.3-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7204 Apr 26 19:00 ragout_2.3-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1826 Apr 26 19:00 ragout_2.3-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 2113576 Apr 26 19:00 ragout_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1315 Apr 26 19:00 ragout_2.3-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2: total 21496 -rw-r--r-- 1 jenkins jenkins 72665 Apr 26 19:02 build.log -rw-r--r-- 1 jenkins jenkins 1304292 Apr 26 19:02 ragout-dbgsym_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Apr 26 19:02 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Apr 26 19:02 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Apr 26 19:02 ragout_2.3-5.dsc -rw-r--r-- 1 jenkins jenkins 6322 Apr 26 19:02 ragout_2.3-5_arm64.buildinfo -rw-r--r-- 1 jenkins jenkins 7204 Apr 26 19:02 ragout_2.3-5_arm64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1826 Apr 26 19:02 ragout_2.3-5_arm64.changes -rw-r--r-- 1 jenkins jenkins 2113576 Apr 26 19:02 ragout_2.3-5_arm64.deb -rw-r--r-- 1 jenkins jenkins 1315 Apr 26 19:02 ragout_2.3-5_source.changes Sat Apr 26 19:02:47 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Sat Apr 26 19:02:48 UTC 2025 I: ragout_2.3-5_arm64.changes: Format: 1.8 Date: Fri, 02 Feb 2024 11:01:34 +0100 Source: ragout Binary: ragout ragout-dbgsym ragout-examples Architecture: arm64 all Version: 2.3-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: ragout - Reference-Assisted Genome Ordering UTility ragout-examples - Reference-Assisted Genome Ordering UTility (example data) Closes: 1061835 Changes: ragout (2.3-5) unstable; urgency=medium . * Port to Python3.12 by removing vendored six.py Closes: #1061835 * Standards-Version: 4.6.2 (routine-update) * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) Checksums-Sha1: e0ebdc31362ba129de2eab70449b329dea2451e6 1304292 ragout-dbgsym_2.3-5_arm64.deb 6ce748ca806e517376280c69bce85b08262f28ad 18434304 ragout-examples_2.3-5_all.deb d808a8f7414893d223127e746918af8813c411ad 6322 ragout_2.3-5_arm64.buildinfo d45ce977b9515ac929f3bba855cfc372c2bc3a00 2113576 ragout_2.3-5_arm64.deb Checksums-Sha256: d853d46729af9b7ecd4333a4d31c8ca112a81de0b45ebefb1cdc2168a85ce75a 1304292 ragout-dbgsym_2.3-5_arm64.deb e8c043fa193a49b9dcca59eac3a61b26802744981f6dfd4572cb8811e5776222 18434304 ragout-examples_2.3-5_all.deb 650e283683839205c7c20e55d5464012f7e9408142a93e0f04f7f8d25f706cc3 6322 ragout_2.3-5_arm64.buildinfo 84e5eaddb003b5ec8bca69b8113962fe08eb80b3184a645aaa61125d7853c9dc 2113576 ragout_2.3-5_arm64.deb Files: c7b3cb297c78179de0878cd479139d7b 1304292 debug optional ragout-dbgsym_2.3-5_arm64.deb edbf05d03d0e9db45e3b97b13f76ae06 18434304 science optional ragout-examples_2.3-5_all.deb 2ede675deb911647fc73716836610ae8 6322 science optional ragout_2.3-5_arm64.buildinfo 843489b7e8a9acd601886b8659edface 2113576 science optional ragout_2.3-5_arm64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ragout_2.3-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ragout_2.3-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/ragout_2.3-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/arm64/ragout_2.3-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/arm64/ragout_2.3-5_arm64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/ragout_2.3-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-04-26 19:00:22.097634544 +0000 +++ b2/build.log 2025-04-26 19:02:40.846670362 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Apr 26 06:58:14 -12 2025 -I: pbuilder-time-stamp: 1745693894 +I: Current time: Sat May 30 15:23:25 +14 2026 +I: pbuilder-time-stamp: 1780104205 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,52 +25,84 @@ dpkg-source: info: applying python3.12.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/463253/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 30 01:23 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2956341/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' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='da9751a376d8408986101ddf96d27f74' - 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='463253' - PS1='# ' - PS2='> ' + INVOCATION_ID=8f9b85855ef841f2892c3dc5d72cb9e9 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2956341 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.AqJWWNr5/pbuilderrc_QvjU --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1 --logfile b1/build.log ragout_2.3-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/pbuilderrc_sMxr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2 --logfile b2/build.log ragout_2.3-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-33-cloud-arm64 #1 SMP Debian 6.1.133-1 (2025-04-10) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/463253/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Mar 4 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -183,7 +215,7 @@ Get: 65 http://deb.debian.org/debian unstable/main arm64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 66 http://deb.debian.org/debian unstable/main arm64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 67 http://deb.debian.org/debian unstable/main arm64 python3-six all 1.17.0-1 [16.5 kB] -Fetched 40.2 MB in 0s (201 MB/s) +Fetched 40.2 MB in 0s (136 MB/s) Preconfiguring packages ... Selecting previously unselected package libpython3.13-minimal: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 ... 19953 files and directories currently installed.) @@ -411,8 +443,8 @@ Setting up tzdata (2025b-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Apr 26 18:58:32 UTC 2025. -Universal Time is now: Sat Apr 26 18:58:32 UTC 2025. +Local time is now: Sat May 30 01:23:44 UTC 2026. +Universal Time is now: Sat May 30 01:23:44 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -478,7 +510,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/ragout-2.3/ && 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 > ../ragout_2.3-5_source.changes +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/ragout-2.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../ragout_2.3-5_source.changes dpkg-buildpackage: info: source package ragout dpkg-buildpackage: info: source version 2.3-5 dpkg-buildpackage: info: source distribution unstable @@ -824,12 +860,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2956341/tmp/hooks/B01_cleanup finished 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/463253 and its subdirectories -I: Current time: Sat Apr 26 07:00:21 -12 2025 -I: pbuilder-time-stamp: 1745694021 +I: removing directory /srv/workspace/pbuilder/2956341 and its subdirectories +I: Current time: Sat May 30 15:25:39 +14 2026 +I: pbuilder-time-stamp: 1780104339 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/ragout_2.3-5.diff: 66.4% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/arm64/ragout_2.3-5.diff.gz b2/build.log: 85.8% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.4% -- replaced with stdout Sat Apr 26 19:02:49 UTC 2025 I: diffoscope 294 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_ragout_unstable_arm64_1745694169 + touch /var/log/reproducible-builds/diffoscope_stamp_ragout_unstable_arm64_1745694169 + RESULT=0 + systemd-run '--description=diffoscope on ragout/2.3-5 in unstable/arm64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-arm64_12-92638 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5 --run-session -c jenkins-reproducible-unstable-diffoscope-d01fd5cc-49e5-4a86-b1f9-3c3596dc086c -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/dbd-tmp-H7AxpNX ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1/ragout_2.3-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2/ragout_2.3-5_arm64.changes' + false + set +x Running as unit: rb-diffoscope-arm64_12-92638.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/ragout_2.3-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b1/ragout_2.3-5_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.AqJWWNr5/b2/ragout_2.3-5_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 Service runtime: 236ms CPU time consumed: 236ms _ _ __ __ _ __ _ ___ _ _| |_ | '__/ _` |/ _` |/ _ \| | | | __| | | | (_| | (_| | (_) | |_| | |_ |_| \__,_|\__, |\___/ \__,_|\__| |___/ Sat Apr 26 19:02:50 UTC 2025 I: diffoscope 294 found no differences in the changes files, and a .buildinfo file also exists. Sat Apr 26 19:02:50 UTC 2025 I: ragout from unstable built successfully and reproducibly on arm64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-04-26 19:02:50] INFO: Starting at 2025-04-26 19:02:50.866836 [2025-04-26 19:02:50] INFO: Generating the pages of 1 package(s) [2025-04-26 19:02:51] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/arm64/ragout didn't produce a buildlog, even though it has been built. [2025-04-26 19:02:51] INFO: Finished at 2025-04-26 19:02:51.222647, took: 0:00:00.355822 Sat Apr 26 19:02:51 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/arm64/ragout.html Sat Apr 26 19:02:51 UTC 2025 I: Submitting .buildinfo files to external archives: Sat Apr 26 19:02:51 UTC 2025 I: Submitting 8.0K b1/ragout_2.3-5_arm64.buildinfo.asc https://buildinfo.debian.net/d808a8f7414893d223127e746918af8813c411ad/ragout_2.3-5_all Sat Apr 26 19:03:10 UTC 2025 I: Submitting 8.0K b2/ragout_2.3-5_arm64.buildinfo.asc Sat Apr 26 19:03:40 UTC 2025 E: Could not submit buildinfo from b2 to http://buildinfo.debian.net/api/submit Sat Apr 26 19:03:40 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Sat Apr 26 19:03:40 UTC 2025 I: Done submitting .buildinfo files. Sat Apr 26 19:03:40 UTC 2025 I: Removing signed ragout_2.3-5_arm64.buildinfo.asc files: removed './b1/ragout_2.3-5_arm64.buildinfo.asc' removed './b2/ragout_2.3-5_arm64.buildinfo.asc' 1745694220 arm64 unstable ragout Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ragout_2.3-5.rbuild.log: 83.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/arm64/ragout_2.3-5.rbuild.log.gz [2025-04-26 19:03:40] INFO: Starting at 2025-04-26 19:03:40.609180 [2025-04-26 19:03:40] INFO: Generating the pages of 1 package(s) [2025-04-26 19:03:41] INFO: Finished at 2025-04-26 19:03:41.101631, took: 0:00:00.492460 All cleanup done. Sat Apr 26 19:03:41 UTC 2025 - total duration: 0h 4m 55s. Sat Apr 26 19:03:41 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-Ma2ICo3c, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 5min 45.738s CPU time consumed: 8.662s