Running as unit: rb-build-amd64_8-72709.service; invocation ID: 60af520448374a0f9f90252f26ff4256 ==================================================================================== Wed Sep 17 15:23:21 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_8) on jenkins, called using "ionos15-amd64 ionos11-amd64" as arguments. Wed Sep 17 15:23:21 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-oHnAzoQd" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 17 15:23:21 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Sep 17 15:23:21 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-fISMi8' Wed Sep 17 15:23:22 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Sep 17 15:23:22 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-gQVC1I' 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 amd64 on jenkins now. 1st build will be done on ionos15-amd64.debian.net. 2nd build will be done on ionos11-amd64.debian.net. ============================================================================= Wed Sep 17 15:23:45 UTC 2025 I: starting to build ragout/unstable/amd64 on jenkins on '2025-09-17 15:23' Wed Sep 17 15:23:45 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_8/72709/console.log 1758122625 amd64 unstable ragout Wed Sep 17 15:23:45 UTC 2025 I: Downloading source for unstable/ragout=2.3-5 --2025-09-17 15:23:45-- 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% 249M=0s 2025-09-17 15:23:45 (249 MB/s) - ‘ragout_2.3-5.dsc’ saved [2117/2117] --2025-09-17 15:23:45-- 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% 249M=0s 2025-09-17 15:23:45 (249 MB/s) - ‘ragout_2.3-5.dsc’ saved [2117/2117] Wed Sep 17 15:23:45 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----- Wed Sep 17 15:23:45 UTC 2025 I: Checking whether the package is not for us Wed Sep 17 15:23:45 UTC 2025 I: Starting 1st build on remote node ionos15-amd64.debian.net. Wed Sep 17 15:23:45 UTC 2025 I: Preparing to do remote build '1' on ionos15-amd64.debian.net. Wed Sep 17 15:23:45 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Wed Sep 17 15:23:45 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-LLrube' ==================================================================================== Tue Oct 20 21:46:46 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "1 ragout unstable /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q 2.3-5" as arguments. Tue Oct 20 21:46:46 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-wWK7cLy7" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Oct 20 21:46:46 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 (53.0 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 (53.0 MB/s) Download complete and in download only mode ============================================================================= Building ragout in unstable on amd64 on ionos15-amd64 now. Date: Tue Oct 20 21:46:46 UTC 2026 Date UTC: Tue Oct 20 21:46:46 UTC 2026 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 09:46:46 -12 2026 I: pbuilder-time-stamp: 1792532806 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: no acceptable signature found 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/338423/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d688bf23c8c84f1b8c07562519d93cae' 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='338423' 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.ogoUAV6Q/pbuilderrc_xWdX --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.ogoUAV6Q/b1 --logfile b1/build.log ragout_2.3-5.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/338423/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 ... 19917 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-sphinxdoc{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} libxml2-16{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 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, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 41.3 MB of archives. After unpacking 192 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.17.0-1 [16.5 kB] Fetched 41.3 MB in 2s (19.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. 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Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 20 21:48:08 UTC 2026. Universal Time is now: Tue Oct 20 21:48:08 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... 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 (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 amd64 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-x86_64' 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/__init__.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 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/breakpoint_graph.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/inferer.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/repeat_resolver.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/__init__.py -> /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 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/phylogeny_parser.py -> /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/__init__.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 creating /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/inferer.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/__init__.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 creating /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/utils.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 copying ragout/shared/datatypes.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/hal.py -> /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/maf.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/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/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/__init__.py -> /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/lexer.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/DH1.fasta -> /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/mg1655.coords -> /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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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/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/overlap.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/__init__.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/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 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/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/__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/tree.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/main.py -> /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/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/config.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/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/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/__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/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/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/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__ 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__ 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/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/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/__init__.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/__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/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/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/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/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/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/__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/__init__.py -> /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/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/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/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/recipe_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/__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/fasta_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/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 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/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/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/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/repeat_resolver.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/__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/__version__.py -> /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/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 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/inferer.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/__init__.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/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 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 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 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/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/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph 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/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/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/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/__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/tree.py to tree.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/main.py to main.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/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/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/__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/datatypes.py to datatypes.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/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/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/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/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/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/__init__.py to __init__.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/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/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/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/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/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/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/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/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/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/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/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/__version__.py to __version__.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/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/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/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/__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/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/assembly_graph/__init__.py to __init__.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 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_amd64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_amd64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/338423 and its subdirectories I: Current time: Tue Oct 20 09:50:39 -12 2026 I: pbuilder-time-stamp: 1792533039 Tue Oct 20 21:50:39 UTC 2026 I: Signing ./b1/ragout_2.3-5_amd64.buildinfo as ragout_2.3-5_amd64.buildinfo.asc Tue Oct 20 21:50:39 UTC 2026 I: Signed ./b1/ragout_2.3-5_amd64.buildinfo as ./b1/ragout_2.3-5_amd64.buildinfo.asc Tue Oct 20 21:50:39 UTC 2026 - build #1 for ragout/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Tue Oct 20 21:50:39 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-wWK7cLy7, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 15:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 15:23 b2 -rw-rw-r-- 1 jenkins jenkins 2117 Feb 2 2024 ragout_2.3-5.dsc -rw------- 1 jenkins jenkins 3201 Sep 17 15:23 rbuildlog.Rfncglf /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b1: total 21484 -rw-r--r-- 1 jenkins jenkins 69574 Sep 17 15:27 build.log -rw-r--r-- 1 jenkins jenkins 1319692 Sep 17 15:27 ragout-dbgsym_2.3-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Sep 17 15:27 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Sep 17 15:27 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Sep 17 15:27 ragout_2.3-5.dsc -rw-r--r-- 1 jenkins jenkins 6254 Sep 17 15:27 ragout_2.3-5_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7136 Sep 17 15:27 ragout_2.3-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1826 Sep 17 15:27 ragout_2.3-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 2124308 Sep 17 15:27 ragout_2.3-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1315 Sep 17 15:27 ragout_2.3-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b2: total 0 Wed Sep 17 15:27:40 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 09:46:46 -12 2026 I: pbuilder-time-stamp: 1792532806 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: no acceptable signature found 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/338423/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='d688bf23c8c84f1b8c07562519d93cae' 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='338423' 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.ogoUAV6Q/pbuilderrc_xWdX --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.ogoUAV6Q/b1 --logfile b1/build.log ragout_2.3-5.dsc' SUDO_GID='111' SUDO_HOME='/var/lib/jenkins' SUDO_UID='106' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/338423/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 ... 19917 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-sphinxdoc{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} libxml2-16{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 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, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 41.3 MB of archives. After unpacking 192 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.17.0-1 [16.5 kB] Fetched 41.3 MB in 2s (19.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... 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-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. 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Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Oct 20 21:48:08 UTC 2026. Universal Time is now: Tue Oct 20 21:48:08 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... 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 (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/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 amd64 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-x86_64' 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/__init__.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 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/breakpoint_graph.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/inferer.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/repeat_resolver.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/__init__.py -> /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 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/phylogeny_parser.py -> /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/__init__.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 creating /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/inferer.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/__init__.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 creating /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/utils.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 copying ragout/shared/datatypes.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/hal.py -> /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/maf.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/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/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/__init__.py -> /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/lexer.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/DH1.fasta -> /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/mg1655.coords -> /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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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/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/overlap.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/__init__.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/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 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/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/__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/tree.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/main.py -> /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/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/config.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/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/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/__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/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/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/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__ 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__ 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/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/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/__init__.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/__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/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/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/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/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/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/__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/__init__.py -> /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/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/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/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/recipe_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/__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/fasta_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/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 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/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/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/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/repeat_resolver.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/__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/__version__.py -> /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/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 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/inferer.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/__init__.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/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 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 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 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/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/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph 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/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/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/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/__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/tree.py to tree.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/main.py to main.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/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/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/__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/datatypes.py to datatypes.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/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/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/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/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/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/__init__.py to __init__.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/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/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/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/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/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/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/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/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/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/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/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/__version__.py to __version__.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/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/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/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/__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/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/assembly_graph/__init__.py to __init__.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 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_amd64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_amd64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/338423 and its subdirectories I: Current time: Tue Oct 20 09:50:39 -12 2026 I: pbuilder-time-stamp: 1792533039 Wed Sep 17 15:27:40 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos11-amd64.debian.net. Wed Sep 17 15:27:40 UTC 2025 I: Preparing to do remote build '2' on ionos11-amd64.debian.net. Wed Sep 17 15:27:40 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos11-amd64.debian.net is marked as down. Wed Sep 17 15:27:40 UTC 2025 - checking via ssh if ionos11-amd64.debian.net is up. removed '/tmp/read-only-fs-test-D0LxQ9' ==================================================================================== Wed Sep 17 15:27:41 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos11-amd64, called using "2 ragout unstable /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q 2.3-5" as arguments. Wed Sep 17 15:27:41 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-jIN1vviX" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Wed Sep 17 15:27:41 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 (64.9 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 (64.9 MB/s) Download complete and in download only mode ============================================================================= Re-Building ragout in unstable on amd64 on ionos11-amd64 now. Date: Wed Sep 17 15:27:41 UTC 2025 Date UTC: Wed Sep 17 15:27:41 UTC 2025 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/pbuilderrc_VH78 + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${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.ogoUAV6Q/pbuilderrc_VH78 --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.ogoUAV6Q/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: Thu Sep 18 05:27:41 +14 2025 I: pbuilder-time-stamp: 1758122861 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: no acceptable signature found 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/2550392/tmp/hooks/D01_modify_environment starting debug: Running on ionos11-amd64. 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 Sep 17 15:28 /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/2550392/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/2550392/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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=3cba6900f38a4a2093adf12e348e6531 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=2550392 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.ogoUAV6Q/pbuilderrc_VH78 --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.ogoUAV6Q/b2 --logfile b2/build.log ragout_2.3-5.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-sequence-python3, 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 ... 19917 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-sphinxdoc{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} libxml2-16{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 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, 65 newly installed, 0 to remove and 0 not upgraded. Need to get 41.3 MB of archives. After unpacking 192 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.2-1 [111 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.7-1 [864 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.7-1 [2216 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.13.7-1 [27.2 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 media-types all 13.0.0 [29.3 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 netbase all 6.5 [12.4 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 tzdata all 2025b-5 [260 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.3-3 [74.8 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.3-3 [191 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.7-1 [1960 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.7-1 [761 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.13.7-1 [10.2 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.13.7-1 [28.3 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 36 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20250414 [116 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.7.2-1 [165 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.2.3-6 [27.5 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.7-1 [2162 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.7-1 [5279 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.13.7-1 [10.5 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.7-1 [504 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.13.7-1 [26.1 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.8.0-1 [71.7 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.15.0-1 [92.4 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.4-1 [37.1 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.5.0-1 [33.0 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 78.1.1-0.1 [224 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.23.0-1 [11.0 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 78.1.1-0.1 [738 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.17.0-1 [16.5 kB] Fetched 41.3 MB in 1s (38.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) Preparing to unpack .../libexpat1_2.7.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.2-1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.7-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.7-1_amd64.deb ... Unpacking python3.13-minimal (3.13.7-1) ... Setting up libpython3.13-minimal:amd64 (3.13.7-1) ... Setting up libexpat1:amd64 (2.7.2-1) ... Setting up python3.13-minimal (3.13.7-1) ... 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 ... 20251 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.13.7-1_amd64.deb ... Unpacking python3-minimal (3.13.7-1) ... 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-5_all.deb ... Unpacking tzdata (2025b-5) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../4-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.3-3_all.deb ... Unpacking readline-common (8.3-3) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../6-libreadline8t64_8.3-3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.3-3) ... Selecting previously unselected package libpython3.13-stdlib:amd64. Preparing to unpack .../7-libpython3.13-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3.13-stdlib:amd64 (3.13.7-1) ... Selecting previously unselected package python3.13. Preparing to unpack .../8-python3.13_3.13.7-1_amd64.deb ... Unpacking python3.13 (3.13.7-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.13.7-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.13.7-1) ... Setting up python3-minimal (3.13.7-1) ... 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 ... 21266 files and directories currently installed.) Preparing to unpack .../00-python3_3.13.7-1_amd64.deb ... Unpacking python3 (3.13.7-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../06-libuchardet0_0.0.8-2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../09-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../11-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../12-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../13-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. 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Preparing to unpack .../32-libjs-sphinxdoc_8.2.3-6_all.deb ... Unpacking libjs-sphinxdoc (8.2.3-6) ... Selecting previously unselected package libpython3.13:amd64. Preparing to unpack .../33-libpython3.13_3.13.7-1_amd64.deb ... Unpacking libpython3.13:amd64 (3.13.7-1) ... Selecting previously unselected package zlib1g-dev:amd64. Preparing to unpack .../34-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ... Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Selecting previously unselected package libpython3.13-dev:amd64. Preparing to unpack .../35-libpython3.13-dev_3.13.7-1_amd64.deb ... Unpacking libpython3.13-dev:amd64 (3.13.7-1) ... Selecting previously unselected package libpython3-dev:amd64. Preparing to unpack .../36-libpython3-dev_3.13.7-1_amd64.deb ... Unpacking libpython3-dev:amd64 (3.13.7-1) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../37-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 .../38-python3.13-dev_3.13.7-1_amd64.deb ... Unpacking python3.13-dev (3.13.7-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../39-python3-dev_3.13.7-1_amd64.deb ... Unpacking python3-dev (3.13.7-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../40-python3-more-itertools_10.8.0-1_all.deb ... Unpacking python3-more-itertools (10.8.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../41-python3-typing-extensions_4.15.0-1_all.deb ... Unpacking python3-typing-extensions (4.15.0-1) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../42-python3-typeguard_4.4.4-1_all.deb ... Unpacking python3-typeguard (4.4.4-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../43-python3-inflect_7.5.0-1_all.deb ... Unpacking python3-inflect (7.5.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../44-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 .../45-python3-pkg-resources_78.1.1-0.1_all.deb ... Unpacking python3-pkg-resources (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.text. Preparing to unpack .../46-python3-jaraco.text_4.0.0-1_all.deb ... Unpacking python3-jaraco.text (4.0.0-1) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../47-python3-zipp_3.23.0-1_all.deb ... Unpacking python3-zipp (3.23.0-1) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../48-python3-setuptools_78.1.1-0.1_all.deb ... Unpacking python3-setuptools (78.1.1-0.1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../49-python3-jaraco.context_6.0.1-1_all.deb ... Unpacking python3-jaraco.context (6.0.1-1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../50-python3-networkx_3.2.1-5_all.deb ... Unpacking python3-networkx (3.2.1-5) ... Selecting previously unselected package python3-six. Preparing to unpack .../51-python3-six_1.17.0-1_all.deb ... Unpacking python3-six (1.17.0-1) ... Setting up media-types (13.0.0) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Sep 17 15:29:11 UTC 2025. Universal Time is now: Wed Sep 17 15:29:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... Setting up libexpat1-dev:amd64 (2.7.2-1) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up libjs-sphinxdoc (8.2.3-6) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up netbase (6.5) ... Setting up readline-common (8.3-3) ... 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 (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libreadline8t64:amd64 (8.3-3) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libpython3.13-stdlib:amd64 (3.13.7-1) ... Setting up libpython3-stdlib:amd64 (3.13.7-1) ... Setting up libpython3.13:amd64 (3.13.7-1) ... Setting up python3.13 (3.13.7-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up python3 (3.13.7-1) ... Setting up python3-zipp (3.23.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-six (1.17.0-1) ... Setting up libpython3.13-dev:amd64 (3.13.7-1) ... Setting up python3-typing-extensions (4.15.0-1) ... Setting up dh-python (6.20250414) ... Setting up python3-more-itertools (10.8.0-1) ... Setting up libpython3-dev:amd64 (3.13.7-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.1-1) ... Setting up python3.13-dev (3.13.7-1) ... Setting up python3-typeguard (4.4.4-1) ... Setting up debhelper (13.26) ... Setting up python3-inflect (7.5.0-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.13.7-1) ... Setting up python3-pkg-resources (78.1.1-0.1) ... Setting up python3-setuptools (78.1.1-0.1) ... Setting up python3-networkx (3.2.1-5) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/2550392/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 amd64 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-x86_64' 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/__init__.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/main.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/__init__.py -> /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 creating /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 copying ragout/breakpoint_graph/permutation.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/chimera_detector.py -> /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/inferer.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/__init__.py -> /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 creating /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 copying ragout/overlap/overlap.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/__init__.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/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 creating /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 copying ragout/phylogeny/phylogeny.py -> /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 creating /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 copying ragout/scaffolder/scaffolder.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/output_generator.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/__init__.py -> /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/config.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 creating /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 copying ragout/synteny_backend/maf.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/synteny_backend.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/sibelia.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/__init__.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/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/lexer.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/__init__.py -> /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 creating /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/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/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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 -fcf-protection -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 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 creating /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/__init__.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/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/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/parsers 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 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/recipe_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 creating /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/__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/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/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_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/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/DH1.fasta -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/tests/data creating /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/__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 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__ creating /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/__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 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/inferer.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/__version__.py -> /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/breakpoint_graph 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/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/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 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/repeat_resolver.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/main.py -> /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/synteny_backend 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/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/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/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/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/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/sibelia.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/__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/shared 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/datatypes.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 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/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/debug.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/maf2synteny 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/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__ creating /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/__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/scaffolder.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 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/output_generator.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/newick 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/parser.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/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/tree.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/lexer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick 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/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/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/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/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/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/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/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/__version__.py to __version__.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/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/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/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/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/main.py to main.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/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/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/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/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/sibelia.py to sibelia.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/datatypes.py to datatypes.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/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/debug.py to debug.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/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/scaffolder.py to scaffolder.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/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/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/tree.py to tree.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/lexer.py to lexer.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 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_amd64.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_amd64.deb'. dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_amd64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/2550392/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/2550392 and its subdirectories I: Current time: Thu Sep 18 05:31:37 +14 2025 I: pbuilder-time-stamp: 1758123097 + false + set +x Wed Sep 17 15:31:37 UTC 2025 I: Signing ./b2/ragout_2.3-5_amd64.buildinfo as ragout_2.3-5_amd64.buildinfo.asc Wed Sep 17 15:31:37 UTC 2025 I: Signed ./b2/ragout_2.3-5_amd64.buildinfo as ./b2/ragout_2.3-5_amd64.buildinfo.asc Wed Sep 17 15:31:37 UTC 2025 - build #2 for ragout/unstable/amd64 on ionos11-amd64 done. Starting cleanup. All cleanup done. Wed Sep 17 15:31:37 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-jIN1vviX, removing. /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q: total 88 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 15:27 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 17 15:31 b2 -rw-rw-r-- 1 jenkins jenkins 2117 Feb 2 2024 ragout_2.3-5.dsc -rw------- 1 jenkins jenkins 73064 Sep 17 15:27 rbuildlog.Rfncglf /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b1: total 21520 -rw-r--r-- 1 jenkins jenkins 69574 Sep 17 15:27 build.log -rw-r--r-- 1 jenkins jenkins 1319692 Sep 17 15:27 ragout-dbgsym_2.3-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Sep 17 15:27 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Sep 17 15:27 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Sep 17 15:27 ragout_2.3-5.dsc -rw-r--r-- 1 jenkins jenkins 6254 Sep 17 15:27 ragout_2.3-5_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7136 Sep 17 15:27 ragout_2.3-5_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1826 Sep 17 15:27 ragout_2.3-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 2124308 Sep 17 15:27 ragout_2.3-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 1315 Sep 17 15:27 ragout_2.3-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b2: total 21488 -rw-rw-r-- 1 jenkins jenkins 71504 Sep 17 15:31 build.log -rw-r--r-- 1 jenkins jenkins 1319692 Sep 17 15:31 ragout-dbgsym_2.3-5_amd64.deb -rw-r--r-- 1 jenkins jenkins 18434304 Sep 17 15:31 ragout-examples_2.3-5_all.deb -rw-r--r-- 1 jenkins jenkins 14976 Sep 17 15:31 ragout_2.3-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2117 Sep 17 15:31 ragout_2.3-5.dsc -rw-rw-r-- 1 jenkins jenkins 6254 Sep 17 15:31 ragout_2.3-5_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7136 Sep 17 15:31 ragout_2.3-5_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1826 Sep 17 15:31 ragout_2.3-5_amd64.changes -rw-r--r-- 1 jenkins jenkins 2124308 Sep 17 15:31 ragout_2.3-5_amd64.deb -rw-rw-r-- 1 jenkins jenkins 1315 Sep 17 15:31 ragout_2.3-5_source.changes Wed Sep 17 15:31:38 UTC 2025 I: Deleting $TMPDIR on ionos11-amd64.debian.net. Wed Sep 17 15:31:38 UTC 2025 I: ragout_2.3-5_amd64.changes: Format: 1.8 Date: Fri, 02 Feb 2024 11:01:34 +0100 Source: ragout Binary: ragout ragout-dbgsym ragout-examples Architecture: amd64 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: bff17eb1d77233661c7dfe08965d9d088e186344 1319692 ragout-dbgsym_2.3-5_amd64.deb 6ce748ca806e517376280c69bce85b08262f28ad 18434304 ragout-examples_2.3-5_all.deb 0f18e132851e76025e9b5dea52907e2c4c47632b 6254 ragout_2.3-5_amd64.buildinfo de07c987a9195bdede33e743dbac3fd323078965 2124308 ragout_2.3-5_amd64.deb Checksums-Sha256: 3751750b60f6b7aad0c149a0d47efe04f1a3bfed089e07957f4e9d40f8526502 1319692 ragout-dbgsym_2.3-5_amd64.deb e8c043fa193a49b9dcca59eac3a61b26802744981f6dfd4572cb8811e5776222 18434304 ragout-examples_2.3-5_all.deb 7696e6999713160d96480f47009ff66e40d575f557a0f886e6f1b22e186de6d9 6254 ragout_2.3-5_amd64.buildinfo f7476787bc15ee498ba25d8ead075f58036d02d5fa1e4d7778562cecb764ccd5 2124308 ragout_2.3-5_amd64.deb Files: 08054808ecf150ff7f9f73df22d9b5fd 1319692 debug optional ragout-dbgsym_2.3-5_amd64.deb edbf05d03d0e9db45e3b97b13f76ae06 18434304 science optional ragout-examples_2.3-5_all.deb 40685755bc47fec18218e1b26aaec11a 6254 science optional ragout_2.3-5_amd64.buildinfo dbb828ac1b83a7badf43b3771804818b 2124308 science optional ragout_2.3-5_amd64.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ragout_2.3-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ragout_2.3-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/ragout_2.3-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/ragout_2.3-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/ragout_2.3-5_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ragout_2.3-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-17 15:27:40.059348080 +0000 +++ b2/build.log 2025-09-17 15:31:38.023644242 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Oct 20 09:46:46 -12 2026 -I: pbuilder-time-stamp: 1792532806 +I: Current time: Thu Sep 18 05:27:41 +14 2025 +I: pbuilder-time-stamp: 1758122861 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ 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/338423/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/D01_modify_environment starting +debug: Running on ionos11-amd64. +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 Sep 17 15:28 /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/2550392/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='amd64' + 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]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d688bf23c8c84f1b8c07562519d93cae' - 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='338423' - PS1='# ' - PS2='> ' + INVOCATION_ID=3cba6900f38a4a2093adf12e348e6531 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=2550392 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.ogoUAV6Q/pbuilderrc_xWdX --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.ogoUAV6Q/b1 --logfile b1/build.log ragout_2.3-5.dsc' - SUDO_GID='111' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.ogoUAV6Q/pbuilderrc_VH78 --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.ogoUAV6Q/b2 --logfile b2/build.log ragout_2.3-5.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/338423/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2550392/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -182,7 +214,7 @@ Get: 63 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.1-1 [8276 B] Get: 64 http://deb.debian.org/debian unstable/main amd64 python3-networkx all 3.2.1-5 [13.0 MB] Get: 65 http://deb.debian.org/debian unstable/main amd64 python3-six all 1.17.0-1 [16.5 kB] -Fetched 41.3 MB in 2s (19.0 MB/s) +Fetched 41.3 MB in 1s (38.0 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19917 files and directories currently installed.) @@ -405,8 +437,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Oct 20 21:48:08 UTC 2026. -Universal Time is now: Tue Oct 20 21:48:08 UTC 2026. +Local time is now: Wed Sep 17 15:29:11 UTC 2025. +Universal Time is now: Wed Sep 17 15:29:11 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20240727.1) ... @@ -469,7 +501,11 @@ 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/2550392/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2550392/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 @@ -504,66 +540,66 @@ 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/__init__.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/main.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 +copying ragout/assembly_graph/assembly_refine.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/breakpoint_graph.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 copying ragout/breakpoint_graph/permutation.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/breakpoint_graph.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/repeat_resolver.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 +copying ragout/breakpoint_graph/inferer.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/__init__.py -> /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 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 +copying ragout/overlap/overlap.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/__init__.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/recipe_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 copying ragout/parsers/fasta_parser.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/__init__.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/inferer.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/__init__.py -> /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/merge_iters.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 creating /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/utils.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 copying ragout/shared/datatypes.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/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 creating /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/synteny_backend.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 copying ragout/synteny_backend/maf.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/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 +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/hal.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 creating /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/__init__.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/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/lexer.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 +copying ragout/tests/test_toy.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/DH1.fasta -> /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/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/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' @@ -629,135 +665,135 @@ 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 +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 creating /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/__init__.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/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/overlap.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/__init__.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/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 -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/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/__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/tree.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/main.py -> /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/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/config.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/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/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/__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/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/parsers +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 +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/recipe_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 creating /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/__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/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__ 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/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/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_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/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/__init__.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/__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__ +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 +creating /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/__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 +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__ +creating /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/__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 +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/inferer.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/__version__.py -> /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/breakpoint_graph +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/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/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 +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/repeat_resolver.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/main.py -> /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/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/__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/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/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/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/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/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/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/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/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/__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/__init__.py -> /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/shared +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/datatypes.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 +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/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/debug.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/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/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/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/recipe_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/__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/fasta_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/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 -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/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/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/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/repeat_resolver.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/__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/__version__.py -> /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/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 -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/inferer.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/__init__.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/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__ creating /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/__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/scaffolder.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/merge_iters.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/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 -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/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/assembly_graph/__init__.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/assembly_graph -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/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/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/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/__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/tree.py to tree.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/main.py to main.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/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/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/__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/datatypes.py to datatypes.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/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/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/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/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/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/__init__.py to __init__.cpython-313.pyc +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 +creating /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/__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/parser.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/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/tree.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/lexer.py -> /build/reproducible-path/ragout-2.3/debian/tmp/usr/lib/python3.13/dist-packages/ragout/newick 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/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/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/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/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/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/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/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/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/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/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/__version__.py to __version__.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/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/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/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/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/__version__.py to __version__.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/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/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/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/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/main.py to main.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/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/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/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/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/sibelia.py to sibelia.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/datatypes.py to datatypes.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/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/debug.py to debug.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/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/scaffolder.py to scaffolder.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/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/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/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/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/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/tree.py to tree.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/lexer.py to lexer.cpython-313.pyc running install_egg_info running egg_info creating ragout.egg-info @@ -802,8 +838,8 @@ dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ragout' in '../ragout_2.3-5_amd64.deb'. -dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-deb: building package 'ragout-dbgsym' in '../ragout-dbgsym_2.3-5_amd64.deb'. +dpkg-deb: building package 'ragout-examples' in '../ragout-examples_2.3-5_all.deb'. dpkg-genbuildinfo --build=binary -O../ragout_2.3-5_amd64.buildinfo dpkg-genchanges --build=binary -O../ragout_2.3-5_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -811,12 +847,14 @@ 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/2550392/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2550392/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/338423 and its subdirectories -I: Current time: Tue Oct 20 09:50:39 -12 2026 -I: pbuilder-time-stamp: 1792533039 +I: removing directory /srv/workspace/pbuilder/2550392 and its subdirectories +I: Current time: Thu Sep 18 05:31:37 +14 2025 +I: pbuilder-time-stamp: 1758123097 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ragout_2.3-5.diff: 90.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/ragout_2.3-5.diff.gz b2/build.log: 85.9% -- replaced with stdout Compressing the 1st log... b1/build.log: 86.5% -- replaced with stdout Wed Sep 17 15:31:39 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_ragout_unstable_amd64_1758123099 + touch /var/log/reproducible-builds/diffoscope_stamp_ragout_unstable_amd64_1758123099 + RESULT=0 + systemd-run '--description=diffoscope on ragout/2.3-5 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_8-72709 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q --run-session -c jenkins-reproducible-unstable-diffoscope-f97099ba-00a1-4e9e-87f1-c40c2ee21188 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/dbd-tmp-2MTAlzz ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b1/ragout_2.3-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b2/ragout_2.3-5_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_8-72709.service; invocation ID: 039cc1885de342f58764490b92198a89 # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/ragout_2.3-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b1/ragout_2.3-5_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.ogoUAV6Q/b2/ragout_2.3-5_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 209ms CPU time consumed: 168ms Memory peak: 17.7M (swap: 0B) _ _ __ __ _ __ _ ___ _ _| |_ | '__/ _` |/ _` |/ _ \| | | | __| | | | (_| | (_| | (_) | |_| | |_ |_| \__,_|\__, |\___/ \__,_|\__| |___/ Wed Sep 17 15:31:39 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Wed Sep 17 15:31:39 UTC 2025 I: ragout from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-17 15:31:39] INFO: Starting at 2025-09-17 15:31:39.890182 [2025-09-17 15:31:40] INFO: Generating the pages of 1 package(s) [2025-09-17 15:31:40] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/ragout didn't produce a buildlog, even though it has been built. [2025-09-17 15:31:40] INFO: Finished at 2025-09-17 15:31:40.129126, took: 0:00:00.238947 Wed Sep 17 15:31:40 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/ragout.html Wed Sep 17 15:31:40 UTC 2025 I: Removing signed ragout_2.3-5_amd64.buildinfo.asc files: removed './b1/ragout_2.3-5_amd64.buildinfo.asc' removed './b2/ragout_2.3-5_amd64.buildinfo.asc' 1758123100 amd64 unstable ragout Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ragout_2.3-5.rbuild.log: 83.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/ragout_2.3-5.rbuild.log.gz [2025-09-17 15:31:40] INFO: Starting at 2025-09-17 15:31:40.447056 [2025-09-17 15:31:40] INFO: Generating the pages of 1 package(s) [2025-09-17 15:31:40] INFO: Finished at 2025-09-17 15:31:40.679969, took: 0:00:00.232916 All cleanup done. Wed Sep 17 15:31:40 UTC 2025 - total duration: 0h 8m 18s. Wed Sep 17 15:31:40 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-oHnAzoQd, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 8min 19.021s CPU time consumed: 3.474s Memory peak: 82.6M (swap: 0B)